We thank the Caenorhabditis Genetics Center, funded by the NIH National Center for Research Resources (NCRR), for some of the nematode strains. Monoclonal antibodies developed by H.F. Epstein were obtained from the Developmental Studies Hybridoma Bank developed under the auspices of the NICHD and maintained by the Department of Biology, University of Iowa. This research was supported by a grant from the Israel Science Foundation (grant No. 278/18) and by a grant from the Israel Ministry of Science &#38; Technology, and the Ministry of Foreign Affairs and International Cooperation, General Directorate for Country Promotion, Italian Republic (grant No. 3-14337). We thank members of the Ben-Zvi laboratory for help in preparing this manuscript.

1. Preparation of nematode growth media plates for RNAi
<ol>
	<li>To a 1 L bottle, add 3 g of NaCl, 2.5 g of Bacto-Peptone, 17 g of agar and distilled water up to 1 L and autoclave.</li>
	<li>Cool bottle to 55 &#176;C.</li>
	<li>Add 25 mL of 1 M KH2PO4, pH 6.0, 1 mL of 1 M CaCl2, 1 mL of 1 M MgSO4, and 1 mL of cholesterol solution (Table 1) to make nematode growth media (NGM).</li>
	<li>Add 1 mL of ampicillin (100 mg/mL) and 0.5 mL of 1 M IPTG (Table 1) to make NGM-RNAi solution. 
	NOTE: Commonly used HT115(DE3) E. coli bacteria contain an IPTG-inducible T7 DNA polymerase used for expressing the dsRNA-encoding plasmids. These plasmids also encode for ampicillin resistance.</li>
	<li>Mix the warm solution by swirling the bottle.</li>
	<li>In the hood or using sterile procedures, pour the NGM solution into plates or using a peristaltic pump, dispense the solution into plates. Use 6-well, 12-well, 40 mm or 60 mm plates for this screen. Agar should fill about 2/3 of the plate depth.</li>
	<li>Let the plates dry overnight on the bench at room temperature, keeping the plates covered. NGM plates for RNAi can be stored at 4 &#176;C for up to a month.</li>
</ol>
2. Growing RNAi bacteria and seeding the plates
<ol>
	<li>In the hood or using sterile procedures, add 1 mL of ampicillin (100 mg/mL) and 2.5 mL of tetracycline (5 mg/mL) (Table 1) to a pre-autoclaved 1 L of LB solution and mix. 
	NOTE: Commonly used HT115(DE3) E. coli bacteria are tetracycline-resistant.</li>
	<li>In the hood or using sterile procedures, add 600 &#181;L of LB solution to each well in 2 mL-deep 96-well sterile plates. It is best to use a multichannel pipet for dispensing the media.</li>
	<li>Using sterile procedures, inoculate wells with HT115(DE3) E. coli bacteria transformed with a dsRNA-encoding plasmid targeting a gene of interest or an empty plasmid, as a control. Cover the plates and incubate at 37 &#176;C overnight. Libraries that consist of bacterial clones expressing dsRNA, corresponding to ~94% of predicted C. elegans genes were previously constructed22,23 and are commercially available. The chaperone library used here was constructed by Dr. Richard Morimoto laboratory26.</li>
	<li>Using sterile procedures, seed 75, 150 or 250 &#181;L of bacteria onto the 12-well, 40 mm and 6-well or 60 mm NGM RNAi plates, respectively. Clearly mark the name of the target gene on the plate. Bacteria should cover 30-50% of the agar surface and should not touch the edges of the plate.</li>
	<li>Allow plates to dry for at least 2 days on the bench at room temperature, keeping the plates covered. 
	NOTE: Plates can be incubated at 37 &#176;C overnight. Make sure the inner wells are dry before using or storing the plates. For all long-term purposes (i.e., drying or storage) keep the plates in the dark. Dried, seeded plates can be stored at 4 &#176;C for up to a month.</li>
</ol>
3. Non-stressful synchronization of embryos
<ol>
	<li>Use a worm pick to move about 100 eggs from an unsynchronized worm plate to a newly seeded NGM plate.</li>
	<li>Cultivate animals for 5 days at 15 &#176;C, 3.5 days at 20 &#176;C or 2.5 days at 25 &#176;C. Animals should reach the first day of egg laying. 
	NOTE: Worms are commonly cultivated at 20 &#176;C. However, different chaperone mutant strains may require specific cultivation temperatures. For example, many temperature-sensitive strains are cultivated at 15 &#176;C but shifted to 25 &#176;C to expose their phenotype.</li>
	<li>Add 1 mL of M9 buffer (Table 1) slowly and away from the bacterial lawn. Rotate the plate so that the buffer completely covers the plate. Then tilt it to one side and remove the liquid from the plate and wash the animals off the plate. 
	NOTE: When using temperature-sensitive animals or chaperone mutants, it is best to maintain the buffers used in the protocol at the animals&#8217; cultivation temperature.</li>
	<li>Repeat step 3.3 three times or until all the animals are washed off the plate.</li>
	<li>Using a standard plastic tip, cut a square of agar from the washed plate where eggs are concentrated and place the piece of agar onto a newly seeded NGM plate. 
	NOTE: ~200 eggs are required to produce enough egg-laying animals; too many animals consume the bacteria too quickly. Low food levels can impact proteostasis27.</li>
	<li>Cultivate the animals for 5 days at 15 &#176;C, 3.5 days at 20 &#176;C or 2.5 days at 25 &#176;C. At this point, the plates should be covered with synchronized eggs. 
	NOTE: Animals can be shifted to a new plate for a short duration for a more stringent synchronization. However, it is important to only use adults at the early stages of egg-laying as animals can retain eggs in their uterus impacting synchronization.</li>
	<li>Add 1 mL of M9 buffer slowly and away from the bacterial lawn.</li>
	<li>Rotate the plate so that the buffer completely covers the plate. Then tilt it to one side and remove the liquid from the plate and wash the animals off the plate.</li>
	<li>Repeat step 3.7 three times or until all animals are washed off the plate.</li>
	<li>Add 1 mL of M9 buffer and use a cell scraper to release the eggs from the plate.</li>
	<li>Collect the M9 buffer containing the eggs from the plates.</li>
	<li>Centrifuge the M9 buffer containing the eggs at 3,000 x g for 2 min.</li>
	<li>Remove the supernatant and add M9 buffer to reach a volume of 1 mL.</li>
	<li>Resuspend the eggs to disrupt any chunks of eggs and bacteria.</li>
	<li>Repeat the washing procedure described in steps 3.11-3.13 five times. The egg pellet should appear white. If it is still yellow/brown, repeat the wash until a white pellet is attained. 
	NOTE: Bacteria that remain on the eggs can contaminate the dsRNA-expressing bacteria.</li>
	<li>Remove most of the supernatant, leaving about 200 &#181;L. Synchronized eggs can be used for RNAi screens.</li>
</ol>
4. Common phenotypic assays
<ol>
	<li>Cultivation of animals during experiments
	<ol>
		<li>Place a drop of ~30 eggs close to the bacterial lawn in each RNAi-seeded plate. For reference, also place ~30 eggs on plates seeded with empty vector-containing (L4440) bacteria.</li>
		<li>Cultivate age-synchronized animals on NGM RNAi-seeded plates. The duration of the experiment will depend on the stage at which the animals are to be monitored and the temperature of cultivation. Adjust the cultivation temperature when using temperature-sensitive mutant animals. Adjust the cultivation duration when using developmentally delayed mutant animals. 
		NOTE: While timing can vary, once animals reach adulthood, egg laying (and the resulting rapid food consumption), as well as age-dependent proteostsis collapse28, could impact the results. It is thus recommended to score animals before the onset of egg laying (day 1 of adulthood). Wild type animals reach this stage after 4.5 days at 15 &#176;C, 3 days at 20 &#176;C or 2 days at 25 &#176;C.</li>
		<li>The number of repeats used will depend on the size of the gene set examined. For the chaperone library (97 genes), repeat experiments at least four times. The size of the population depends on the assay used. In the behavioral assays discussed here, score &#62;15 animals per experimental condition in each repeat. Data and statistical analyses also strongly depend on the type of assay used. Data in the assays discussed here can be presented as means &#177; SEM.</li>
		<li>Compare the RNAi- and empty vector control-treated animals as independent populations. P values can be calculated using one-way or two-way ANOVA, depending on the changes examined, namely aggravating or alleviating alone or both. When examining a single RNAi treatment vs. control, P values can be calculated using one-way or two-way Mann-Whitney rank sum test. Other than statistical significance, consider a threshold for hits based on the degree of impact on the phenotype.</li>
	</ol>
	</li>
	<li>Developmental arrest/delay
	<ol>
		<li>Cultivate age-synchronized animals as in step 4.1 until animals grown on empty vector-containing control bacteria reach adulthood but before egg laying starts.</li>
		<li>Monitor animals using a stereomicroscope and count the number of larvae and adults to score the percent of developmentally delayed animals. For reference, compare to mutant animals grown on empty vector-containing control bacteria. hsp-1 or hsp-90 RNAi treatment results in developmental arrest of wild type animals and can be used as a positive control.</li>
		<li>To score the percent of developmentally delayed animals over time, repeat step 4.2.2. 
		NOTE: If there are egg-laying adults on the plate, transfer the developmentally delayed animals to a new NGM-RNAi plate labeled for the same target gene to avoid confusion with progeny.</li>
	</ol>
	</li>
	<li>Sterility or egg laying defects
	<ol>
		<li>Cultivate age-synchronized animals as in step 4.1 until animals grown on empty vector-control bacteria begin to lay eggs.</li>
		<li>Monitor animals using a stereomicroscope and score the percent of animals with no visible eggs in their uterus. For reference, compare to mutant animals grown on empty vector-control bacteria.</li>
		<li>Alternately, monitor animals using a stereomicroscope and score the percent of animals with a uterus full of eggs, defined as EGg Laying defective (Egl-d) phenotype29.</li>
	</ol>
	</li>
	<li>Embryonic lethality
	<ol>
		<li>Cultivate age-synchronized animals as in step 4.1 until the animals begin to lay eggs.</li>
		<li>Transfer ~100 eggs to an empty plate. Spread the eggs in rows to simplify counting.</li>
		<li>Score the percent of unhatched eggs on the plate after 24-48 hours. For reference, compare to eggs of animals treated with empty vector-control bacteria.</li>
	</ol>
	</li>
	<li>Paralysis assay
	<ol>
		<li>For day 1 adults, cultivate age-synchronized animals as in step 4.1 until animals grown on empty vector-control bacteria reach adulthood but before egg laying starts.</li>
		<li>Draw a line on the back of a regular NGM agar plate using a fine marker.</li>
		<li>Place 5-10 animals on the marked line.</li>
		<li>Set a timer and wait for 10 min.</li>
		<li>Score the percent of animals remaining on the line as paralyzed worms. For reference, compare to mutant animals grown on empty vector-control bacteria. Wild type animals treated with unc-45 RNAi show severe paralysis phenotype and can be used as a positive control. 
		NOTE: This assay highlights animals showing medium to severe paralysis. Such animals usually lie straight on the plate, rather than presenting the common curved shape. Moreover, a patch cleared of bacteria is visible around the heads of paralyzed worms.</li>
	</ol>
	</li>
	<li>Thrashing assay
	<ol>
		<li>Cultivate age-synchronized animals as in step 4.1 until animals grown on empty vector-control bacteria reach adulthood but before egg laying starts.</li>
		<li>Pipet 100 &#181;L of M9 buffer at the animals&#8217; cultivation temperature into a 96-well plate.</li>
		<li>Place ~15 worms, one per well, into the M9 buffer-containing wells.</li>
		<li>Let the animals adjust for 5 min.</li>
		<li>Examine each animal under the stereomicroscope, start a timer counting down 15 s, and count the number of body bends each animal performs in that timespan. The values counted can be normalized to body bends per min. For reference, compare to mutant animals grown on empty vector-control bacteria. 
		NOTE: This motility assay is very sensitive and can detect very mild differences between treatments. However, motility in liquid and motility on agar can differ.</li>
	</ol>
	</li>
</ol>
5. Validation of protein knockdown
<ol>
	<li>Place 250-300 synchronized eggs onto a 60 mm NGM-RNAi plate seeded with the relevant dsRNA-expressing or empty vector-containing (L4440) bacteria. 
	NOTE: RNAi knockdown could result in aberrant accumulation of embryos, in a lack of embryos or in developmental arrest that could impact gene expression. This should be considered when determining the age of the animals to be examined.</li>
	<li>For day 1 adults, cultivate animals for 4.5 days at 15 &#176;C, 3 days at 20 &#176;C or 2 days at 25 &#176;C.</li>
	<li>Pick and transfer a total of 200 young adult animals into the cap of a 1.5 mL tube fill with 200 &#181;L of PBS-T. 
	NOTE: When using temperature-sensitive animals or chaperone mutants, it is best to maintain the buffers used in the protocol at the animals&#8217; cultivation temperature.</li>
	<li>Close the cap carefully and centrifuge at 1,000 x g for 1 min.</li>
	<li>Add 800 &#181;L of PBS-T (Table 1) and centrifuge at 1,000 x g for 1 min.</li>
	<li>Carefully remove the top 900 &#181;L.</li>
	<li>Repeat steps 5.4-5.6 three times.</li>
	<li>Remove 900 &#181;L, leaving 100 &#181;L of solution containing the 200 worms.</li>
	<li>Add 25 &#181;L of 5x sample buffer (Table 1).</li>
	<li>Heat the samples for 10 min at 92&#176;C while shaking at 1000 rpm. Samples can then be frozen and kept at -20 &#176;C.</li>
	<li>Load 20 &#181;L of each sample and run on an SDS-PAGE gel.</li>
	<li>Perform western blot analysis using appropriate antibodies to determine the relative stability of the protein.</li>
	<li>Determine the intensity of the bands using densitometric software, such as the freely available ImageJ gel module. Normalize all values to those measured in the control sample(s). 
	NOTE: The aim of RNAi knockdown in our screens is to lower protein levels of a specific chaperone/co-chaperone. Thus, the best way to assess the efficiency of the RNAi knockdown is by western blot analysis. This requires specific antibodies. Alternately, qPCR can be used to quantify mRNA levels.</li>
</ol>

The authors have nothing to disclose.

An integrated picture of the proteostasis network reflecting how it is organized and functions in different metazoan cells and tissues remains lacking. To address this shortcoming, specific information on the interactions of various components of this network, such as molecular chaperones, in specific tissues during the course of development and aging is required. Here, we showed how the use of tissue-specific perturbations enabled us to examine the chaperone network in a given tissue. To explore tissue-specific chaperon...

Cells cope with protein damage by employing quality control machineries that repair, sequester or remove any damaged proteins1,2. Folding and assembly of protein complexes are supported by molecular chaperones, a diverse group of highly conserved proteins that can repair or sequester damaged proteins3,4,5,6,7. The removal of damaged proteins is mediated by the ubiquitin-proteasome system (UPS)8 or by the autophagy machinery9 in collaboration with chaperones10,11,12. Protein homeostasis (proteostasis) is, therefore, maintained by quality control networks composed of folding and degradation machineries3,13. However, understanding the interactions between the various components of the proteostasis network in vivo is a major challenge. While protein-protein interaction screens contribute important information on physical interactions and chaperone complexes14,15, understanding the organization and compensatory mechanisms within tissue-specific chaperone networks in vivo is lacking.
Genetic interactions are often used as a powerful tool to examine relationship between pairs of genes that are involved in common or compensatory biological pathways16,17,18. Such relationships can be measured by combining pairs of mutations and quantifying the impact of a mutation in one gene on the phenotypic severity caused by a mutation in the second gene16. While most such combinations do not show any effect in terms of phenotype, some genetic interactions can either aggravate or alleviate the severity of the measured phenotype. Aggravating mutations are observed when the phenotype of the double deletion mutant is more severe than the expected phenotype seen upon combining the single deletion mutants, implying that the two genes function in parallel pathways, together affecting a given function. In contrast, alleviating mutations are observed when the phenotype of the double deletion mutant is less severe than the phenotype seen with the single deletion mutants, implying that the two genes act together as a complex or participate in the same pathway16,18. Accordingly, diverse phenotypes that can be quantified, including broad phenotypes, such as lethality, growth rates and brood size, as well as specific phenotypes, such as transcriptional reporters, have been used to identify genetic interactions. For example, Jonikas et al. relied on an ER stress reporter to examine interactions of the Saccharomyces cerevisiae ER unfolded protein response proteostasis network using pairwise gene deletion analyses19.
Genetic interaction screens involve systematically crossing pairwise deletion mutations to generate a comprehensive set of double mutants20. However, in animal models, and specifically in C. elegans, this large-scale approach is not feasible. Instead, mutant strains can be tested for their genetic interaction patterns by down-regulating gene expression using RNA interference (RNAi)21. C. elegans is a powerful system for screens based on RNAi22,23. In C. elegans, double-stranded RNA (dsRNA) delivery is achieved by bacterial feeding, leading to the spread of dsRNA molecules to numerous tissues. In this manner, the introduced dsRNA molecules impact the animal via a rapid and simple procedure21. A genetic interaction screen using RNAi can, therefore, reveal the impact of down-regulating a set of genes or most C. elegans coding genes using RNAi libraries24. In such a screen, hits that impact the behavior of the mutant of interest but not the wild type strain are potential modifiers of the phenotype being monitored25. Here, we apply a combination of mutations and RNAi screening to systematically map tissue-specific chaperone interactions in C. elegans.

<table>
	<tbody>
		<tr>
			<td>12-well-plates</td>
			<td>SPL</td>
			<td>BA3D16B</td>
			<td></td>
		</tr>
		<tr>
			<td>40 mm plates</td>
			<td>Greiner Bio-one</td>
			<td>627160</td>
			<td></td>
		</tr>
		<tr>
			<td>60 mm plates</td>
			<td>Greiner Bio-one</td>
			<td>628102</td>
			<td></td>
		</tr>
		<tr>
			<td>6-well plates</td>
			<td>Thermo Scientific</td>
			<td>140675</td>
			<td></td>
		</tr>
		<tr>
			<td>96 well 2 mL 128.0/85mm</td>
			<td>Greiner Bio-one</td>
			<td>780278</td>
			<td></td>
		</tr>
		<tr>
			<td>Agar</td>
			<td>Formedium</td>
			<td>AGA03</td>
			<td></td>
		</tr>
		<tr>
			<td>Ampicillin</td>
			<td>Formedium</td>
			<td>69-52-3</td>
			<td></td>
		</tr>
		<tr>
			<td>bromophenol blue</td>
			<td>Sigma</td>
			<td>BO126-25G</td>
			<td></td>
		</tr>
		<tr>
			<td>CaCl2</td>
			<td>Merck</td>
			<td>1.02382.0500</td>
			<td></td>
		</tr>
		<tr>
			<td>Camera</td>
			<td>Qimaging</td>
			<td>q30548</td>
			<td></td>
		</tr>
		<tr>
			<td>Cholesterol</td>
			<td>Amresco</td>
			<td>0433-250G</td>
			<td></td>
		</tr>
		<tr>
			<td>Confocal</td>
			<td>Leica</td>
			<td>DM5500</td>
			<td></td>
		</tr>
		<tr>
			<td>Filter (0.22 &#181;m)</td>
			<td>Sigma</td>
			<td>SCGPUO2RE</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorescent stereomicroscope</td>
			<td>Leica</td>
			<td>MZ165FC</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Frutarom</td>
			<td>2355519000024</td>
			<td></td>
		</tr>
		<tr>
			<td>IPTG</td>
			<td>Formedium</td>
			<td>367-93-1</td>
			<td></td>
		</tr>
		<tr>
			<td>KCl</td>
			<td>Merck</td>
			<td>104936</td>
			<td></td>
		</tr>
		<tr>
			<td>KH2PO4</td>
			<td>Merck</td>
			<td>1.04873.1000</td>
			<td></td>
		</tr>
		<tr>
			<td>KOH</td>
			<td>Bio-Lab</td>
			<td>001649029100</td>
			<td></td>
		</tr>
		<tr>
			<td>MgSO4</td>
			<td>Fisher</td>
			<td>22189-08-8</td>
			<td>Gift from the Morimoto laboratory</td>
		</tr>
		<tr>
			<td>Myosin MHC A (MYO-3) antibody</td>
			<td>Hybridoma Bank</td>
			<td>5-6</td>
			<td></td>
		</tr>
		<tr>
			<td>Na2HPO4&#183;7H2O</td>
			<td>Sigma</td>
			<td>s-0751</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Bio-Lab</td>
			<td>001903029100</td>
			<td></td>
		</tr>
		<tr>
			<td>Peptone</td>
			<td>Merck</td>
			<td>61930705001730</td>
			<td></td>
		</tr>
		<tr>
			<td>Plate pouring pump</td>
			<td>Integra</td>
			<td>does it p920</td>
			<td></td>
		</tr>
		<tr>
			<td>RNAi Chaperone library</td>
			<td>NA</td>
			<td>NA</td>
			<td></td>
		</tr>
		<tr>
			<td>SDS</td>
			<td>VWR Life Science</td>
			<td>0837-500</td>
			<td></td>
		</tr>
		<tr>
			<td>&#223;-mercaptoethanol</td>
			<td>Bio world</td>
			<td>41300000-1</td>
			<td></td>
		</tr>
		<tr>
			<td>stereomicroscope</td>
			<td>Leica</td>
			<td>MZ6</td>
			<td></td>
		</tr>
		<tr>
			<td>Tetracycline</td>
			<td>Duchefa Biochemie</td>
			<td>64-75-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>Bio-Lab</td>
			<td>002009239100</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Fisher</td>
			<td>BP337-500</td>
			<td></td>
		</tr>
	</tbody>
</table>

using caenorhabditis elegans to screen for tissue-specific chaperone interactions

Correct folding and assembly of proteins and protein complexes are essential for cellular function. Cells employ quality control pathways that correct, sequester or eliminate damaged proteins to maintain a healthy proteome, thus ensuring cellular proteostasis and preventing further protein damage. Because of redundant functions within the proteostasis network, screening for detectable phenotypes using knockdown or mutations in chaperone-encoding genes in the multicellular organism Caenorhabditis elegans results in the detection of minor or no phenotypes in most cases. We have developed a targeted screening strategy to identify chaperones required for a specific function and thus bridge the gap between phenotype and function. Specifically, we monitor novel chaperone interactions using RNAi synthetic interaction screens, knocking-down chaperone expression, one chaperone at a time, in animals carrying a mutation in a chaperone-encoding gene or over-expressing a chaperone of interest. By disrupting two chaperones that individually present no gross phenotype, we can identify chaperones that aggravate or expose a specific phenotype when both perturbed. We demonstrate that this approach can identify specific sets of chaperones that function together to modulate the folding of a protein or protein complexes associated with a given phenotype.

Using temperature-sensitive mutations in UNC-45 to screen for aggravating or alleviating interactions under permissive or restrictive conditions, respectively 
Muscle assembly and maintenance offer an effective system to study tissue-specific chaperone interactions. The functional unit of contractile muscles, the sarcomere, presents a crystalline-like arrangement of structural and regulatory proteins. The stability of the motor protein myosin and its incorporation into the thick filaments of contrac...

Watch this Scientific Journal Video about Using Caenorhabditis elegans to Screen for Tissue-Specific Chaperone Interactions at JoVE.com

Using Caenorhabditis elegans to Screen for Tissue-Specific Chaperone Interactions

To study chaperone-chaperone and chaperone-substrate interactions, we perform synthetic interaction screens in Caenorhabditis elegans using RNA interference in combination with mild mutations or over-expression of chaperones and monitor tissue-specific protein dysfunction at the organismal level.

Using Caenorhabditis elegans to Screen for Tissue-Specific Chaperone Interactions

Correct folding and assembly of proteins and protein complexes are essential for cellular function. Cells employ quality control pathways that correct, ...

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2.8K Views.  Ben-Gurion University of the Negev. To study chaperone-chaperone and chaperone-substrate interactions, we perform synthetic interaction screens in Caenorhabditis elegans using RNA interference in combination with mild mutations or over-expression of chaperones and monitor tissue-specific protein dysfunction at the organismal level.

Video: Using Caenorhabditis elegans to Screen for Tissue-Specific Chaperone Interactions

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 ...

Using RNA-mediated Interference Feeding Strategy to Screen for Genes Involved in Body Size Regulation in the Nematode C. elegans

Double-strand RNA-mediated interference (RNAi) is an effective strategy to knock down target gene expression1-3. It has been applied to many model systems including plants, invertebrates and vertebrates. There are various methods to achieve RNAi in vivo4,5. For example, the target gene may be transformed into an RNAi vector, and then either permanently or transiently transformed into cell lines or primary cells to achieve gene knockdown effects; alternatively synthesized double-strand oligonucleotides from specific target genes (RNAi oligos) may be transiently transformed into cell lines or primary cells to silence target genes; or synthesized double-strand RNA molecules may be microinjected into an organism. Since the nematode C. elegans uses bacteria as a food source, feeding the animals with bacteria expressing double-strand RNA against target genes provides a viable strategy6. Here we present an RNAi feeding method to score body size phenotype. Body size in C. elegans is regulated primarily by the TGF- &beta; - like ligand DBL-1, so this assay is appropriate for identification of TGF-&beta; signaling components7. We used different strains including two RNAi hypersensitive strains to repeat the RNAi feeding experiments. Our results showed that rrf-3 strain gave us the best expected RNAi phenotype. The method is easy to perform, reproducible, and easily quantified. Furthermore, our protocol minimizes the use of specialized equipment, so it is suitable for smaller laboratories or those at predominantly undergraduate institutions.

Using RNA-mediated Interference Feeding Strategy to Screen for Genes Involved in Body Size Regulation in the Nematode C. elegans

We demonstrate how to use the RNAi feeding technique to knock down target genes and score body size phenotype in C. elegans. This method could be used for a large scale screen to identify potential genetic components of interest, such as those involved in body size regulation by DBL-1/TGF-&beta; signaling.

Double-strand RNA-mediated interference (RNAi) is an effective strategy to knock down target gene expression1-3. It has been applied to many model systems ...

Using Caenorhabditis elegans as a Model System to Study Protein Homeostasis in a Multicellular Organism

The folding and assembly of proteins is essential for protein function, the long-term health of the cell, and longevity of the organism. Historically, the function and regulation of protein folding was studied in vitro, in isolated tissue culture cells and in unicellular organisms. Recent studies have uncovered links between protein homeostasis (proteostasis), metabolism, development, aging, and temperature-sensing. These findings have led to the development of new tools for monitoring protein folding in the model metazoan organism Caenorhabditis elegans. In our laboratory, we combine behavioral assays, imaging and biochemical approaches using temperature-sensitive or naturally occurring metastable proteins as sensors of the folding environment to monitor protein misfolding. Behavioral assays that are associated with the misfolding of a specific protein provide a simple and powerful readout for protein folding, allowing for the fast screening of genes and conditions that modulate folding. Likewise, such misfolding can be associated with protein mislocalization in the cell. Monitoring protein localization can, therefore, highlight changes in cellular folding capacity occurring in different tissues, at various stages of development and in the face of changing conditions. Finally, using biochemical tools ex vivo, we can directly monitor protein stability and conformation. Thus, by combining behavioral assays, imaging and biochemical techniques, we are able to monitor protein misfolding at the resolution of the organism, the cell, and the protein, respectively.

Using Caenorhabditis elegans as a Model System to Study Protein Homeostasis in a Multicellular Organism

To study the relationship between protein homeostasis, stress and aging, we monitored changes in protein folding by following protein dysfunction, protein localization in the cell and protein stability at the organismal, cellular and protein levels, using the genetically tractable metazoan Caenorhabditis elegans as a model system.

The folding and assembly of proteins is essential for protein function, the long-term health of the cell, and longevity of the organism. Historically, the ...

Dietary Supplementation of Polyunsaturated Fatty Acids in Caenorhabditis elegans

Fatty acids are essential for numerous cellular functions. They serve as efficient energy storage molecules, make up the hydrophobic core of membranes, and participate in various signaling pathways. Caenorhabditis elegans synthesizes all of the enzymes necessary to produce a range of omega-6 and omega-3 fatty acids. This, combined with the simple anatomy and range of available genetic tools, make it an attractive model to study fatty acid function. In order to investigate the genetic pathways that mediate the physiological effects of dietary fatty acids, we have developed a method to supplement the C. elegans diet with unsaturated fatty acids. Supplementation is an effective means to alter the fatty acid composition of worms and can also be used to rescue defects in fatty acid-deficient mutants. Our method uses nematode growth medium agar (NGM) supplemented with fatty acidsodium salts. The fatty acids in the supplemented plates become incorporated into the membranes of the bacterial food source, which is then taken up by the C. elegans that feed on the supplemented bacteria. We also describe a gas chromatography protocol to monitor the changes in fatty acid composition that occur in supplemented worms. This is an efficient way to supplement the diets of both large and small populations of C. elegans, allowing for a range of applications for this method.

Dietary Supplementation of Polyunsaturated Fatty Acids in Caenorhabditis elegans

Caenorhabditis elegans is a useful model to explore the functions of polyunsaturated fatty acids in development and physiology. This protocol describes an efficient method of supplementing the C. elegans diet with polyunsaturated fatty acids.

Fatty acids are essential for numerous cellular functions. They serve as efficient energy storage molecules, make up the hydrophobic core of membranes, ...

A Screenable In Vivo Assay for Mitochondrial Modulators Using Transgenic Bioluminescent Caenorhabditis elegans

The multicellular model organism Caenorhabditis elegans is a small nematode of approximately 1 mm in size in adulthood that is genetically and experimentally tractable. It is economical and easy to culture and dispense in liquid medium which makes it well suited for medium-throughput screening. We have previously validated the use of transgenic luciferase expressing C. elegans strains to provide rapid in vivo assessment of the nematode&#8217;s ATP levels.1-3 Here we present the required materials and procedure to carry out bioassays with the bioluminescent C. elegans strains PE254 or PE255 (or any of their derivative strains). The protocol allows for in vivo detection of sublethal effects of drugs that may identify mitochondrial toxicity, as well as for in vivo detection of potential beneficial drug effects. Representative results are provided for the chemicals paraquat, rotenone, oxaloacetate and for four firefly luciferase inhibitory compounds. The methodology can be scaled up to provide a platform for screening drug libraries for compounds capable of modulating mitochondrial function. Pre-clinical evaluation of drug toxicity is often carried out on immortalized cancerous human cell lines which derive ATP mostly from glycolysis and are often tolerant of mitochondrial toxicants.4,5 In contrast, C. elegans depends on oxidative phosphorylation to sustain development into adulthood, drawing a parallel with humans and providing a unique opportunity for compound evaluation in the physiological context of a whole live multicellular organism.

A Screenable In Vivo Assay for Mitochondrial Modulators Using Transgenic Bioluminescent Caenorhabditis elegans

A protocol is described for in vivo detection of effects of mitochondrial inhibitors in the model organism Caenorhabditis elegans and for identification of potential enhancing compounds. This protocol can be used to screen drug libraries for compounds modulating mitochondrial function.

The multicellular model organism Caenorhabditis elegans is a small nematode of approximately 1 mm in size in adulthood that is genetically and ...

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 ...

Quantifying Tissue-Specific Proteostatic Decline in Caenorhabditis elegans

The ability to maintain proper function and folding of the proteome (protein homeostasis) declines during normal aging, facilitating the onset of a growing number of age-associated diseases. For instance, proteins with polyglutamine expansions are prone to aggregation, as exemplified with the huntingtin protein and concomitant onset of Huntington&#8217;s disease. The age-associated deterioration of the proteome has been widely studied through the use of transgenic Caenorhabditis elegans expressing polyQ repeats fused to a yellow fluorescent protein (YFP). This polyQ::YFP transgenic animal model facilitates the direct quantification of the age-associated decline of the proteome through imaging the progressive formation of fluorescent foci (i.e., protein aggregates) and subsequent onset of locomotion defects that develop as a result of the collapse of the proteome. Further, the expression of the polyQ::YFP transgene can be driven by tissue-specific promoters, allowing the assessment of proteostasis across tissues in the context of an intact multicellular organism. This model is highly amenable to genetic analysis, thus providing an approach to quantify aging that is complementary to lifespan assays. We describe how to accurately measure polyQ::YFP foci formation within either neurons or body wall muscle during aging, and the subsequent onset of behavioral defects. Next, we highlight how these approaches can be adapted for higher throughput, and potential future applications using other emerging strategies for C. elegans genetic analysis.

Quantifying Tissue-Specific Proteostatic Decline in Caenorhabditis elegans

Proteostatic decline is a hallmark of aging, facilitating the onset of neurodegenerative diseases. We outline a protocol to quantifiably measure proteostasis in two different Caenorhabditis elegans tissues through heterologous expression of polyglutamine repeats fused to a fluorescent reporter. This model allows rapid in vivo genetic analysis of proteostasis.

The ability to maintain proper function and folding of the proteome (protein homeostasis) declines during normal aging, facilitating the onset of a ...

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.

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.

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

Using Single-Worm Data to Quantify Heterogeneity in Caenorhabditis elegans-Bacterial Interactions

The nematode Caenorhabditis elegans is a model system for host-microbe and host-microbiome interactions. Many studies to date use batch digests rather than individual worm samples to quantify bacterial load in this organism. Here it is argued that the large inter-individual variability seen in bacterial colonization of the C. elegans intestine is informative, and that batch digest methods discard information that is important for accurate comparison across conditions. As describing the variation inherent to these samples requires large numbers of individuals, a convenient 96-well plate protocol for disruption and colony plating of individual worms is established.

Using Single-Worm Data to Quantify Heterogeneity in Caenorhabditis elegans-Bacterial Interactions

This protocol describes a 96-well disruption of individual bacterially colonized Caenorhabditis elegans following cold paralysis and surface bleaching&#160;to remove external bacteria. The resulting suspension is plated on agar plates to allow accurate, medium-throughput quantification of bacterial load in large numbers of individual worms.

The nematode Caenorhabditis elegans is a model system for host-microbe and host-microbiome interactions. Many studies to date use batch digests rather ...

Quantifying Mitophagy in C. elegans and a Liver Cancer Cell Line

Detection of Mitophagy in Caenorhabditis elegans and Mammalian Cells Using Organelle-Specific Dyes

Mitochondria are essential for various biological functions, including energy production, lipid metabolism, calcium homeostasis, heme biosynthesis, regulated cell death, and the generation of reactive oxygen species (ROS). ROS are vital for key biological processes. However, when uncontrolled, they can lead to oxidative injury, including mitochondrial damage. Damaged mitochondria release more ROS, thereby intensifying cellular injury and the disease state. A homeostatic process named mitochondrial autophagy (mitophagy) selectively removes damaged mitochondria, which are then replaced by new ones. There are multiple mitophagy pathways, with the common endpoint being the breakdown of the damaged mitochondria in lysosomes. 
Several methodologies, including genetic sensors, antibody immunofluorescence, and electron microscopy, use this endpoint to quantify mitophagy. Each method for examining mitophagy has its advantages, such as specific tissue/cell targeting (with genetic sensors) and great detail (with electron microscopy). However, these methods often require expensive resources, trained personnel, and a lengthy preparation time before the actual experiment, such as for creating transgenic animals. Here, we present a cost-effective alternative for measuring mitophagy using commercially available fluorescent dyes targeting mitochondria and lysosomes. This method effectively measures mitophagy in the nematode Caenorhabditis elegans and human liver cells, which indicates its potential efficiency in other model systems.

Author Spotlight: Detection of Mitophagy in Caenorhabditis elegans and Mammalian Cells Using Organelle-Specific Dyes  

Exploring mitophagy through electron microscopy, genetic sensors, and immunofluorescence requires costly equipment, skilled personnel, and a significant time investment. Here, we demonstrate the efficacy of a commercial fluorescence dye kit in quantifying the mitophagy process in both Caenorhabditis elegans and a liver cancer cell line.

Mitochondria are essential for various biological functions, including energy production, lipid metabolism, calcium homeostasis, heme biosynthesis, ...