Name: methods to study changes in inherent protein aggregation with age in caenorhabditis elegans
Uploaded: 2017-11-26T13:00:00
Description: Watch this Scientific Journal Video about Methods to Study Changes in Inherent Protein Aggregation with Age in Caenorhabditis elegans at JoVE.com

This work was supported by funding from the DZNE and a Marie Curie International Reintegration Grant (322120 to D.C.D.)

NOTE: For a better understanding of the procedure, a schematic of the workflow (Figure 1) is attached.
1. Growth of Large Numbers of Young and Aged C. elegans Subjected to RNAi Targeting a Gene of Interest
NOTE: Use C. elegans temperature-induced sterile gon-2(q388) mutants (CF2253) to obtain large aged-synchronized populations. During all steps, it is important to work under semi-sterile conditions with an open...

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Here we report a methodology to isolate highly-insoluble protein aggregates from aging C. elegans subjected to RNAi for analysis by mass spectrometry and Western blotting. We show that improving proteostasis by reducing IIS greatly prevents age-dependent protein aggregation. By selecting specific aggregation-prone proteins to overexpress in C. elegans, it is possible to dissect further the mechanisms modulating inherent protein aggregation.
Inherent Age-dependent Prot...

Protein misfolding and aggregation are recognized as a hallmark of several neurodegenerative diseases such as AD, PD, amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and many others. For instance, &#945;-synuclein assemblies into amyloid fibrils that accumulate as Lewy bodies particularly in the substantia nigra of PD patients, while in ALS patients TDP-43 or FUS misfold to form cytoplasmic aggregates in degenerating motor neurons. In each of these neurodegenerative disorders, mechanisms maintaining protein homeostasis or proteostasis fail to prevent the accumulation of misfolded proteins, consequently leading to disease.
Proteostasis is critical to ensure cellular functions and under normal conditions these regulatory mechanisms tightly control the rate of protein synthesis, folding, and degradation. Several studies demonstrate that with ageing, the ability of many cells and organs to preserve protein homeostasis is gradually compromised and the physiological deterioration of the proteostasis networks with age is an important aggravating factor for neurodegenerative diseases (reviewed in references1,2,3). The fact that the protein quality control and the cellular response to unfolded protein stress are compromised with age suggests that protein misfolding and aggregation could be a general consequence of aging. Indeed, we and others have demonstrated that protein aggregation is not restricted to disease and instead part of the proteome becomes highly detergent-insoluble in aged animals4,5,6,7,8,9,10. Computational and in vivo analysis revealed that these physiological age-related aggregates resemble disease aggregates in several aspects5. The discovery of endogenous, age-dependent protein aggregation gives us the opportunity to dissect the molecular and cellular mechanisms that regulate protein aggregation, without using ectopically expressed human disease-associated proteins. At present, only limited information exists about the regulation of widespread protein insolubility and about the effects of this dysregulation on the health of the organism.
The nematode C. elegans is one of the most extensively studied model organisms in aging research as these animals have a relatively short lifespan and show many characteristic aging features observed in higher organisms. The effects of aging on protein insolubility have been studied in C. elegans by sequential biochemical fractionation based on differential solubility, which is widely used to extract disease aggregates in the field of neurodegeneration research11. By quantitative mass spectrometry, several hundred proteins were shown to become aggregation-prone in C. elegans in the absence of disease5. Here we describe in detail the protocol to grow large numbers of worms in liquid culture and the sequential extraction to isolate aggregated proteins for quantification by mass spectrometry and analysis by Western blot. Because misfolded and aggregation-prone proteins accumulate in aged C. elegans gonads and masks changes in other somatic tissues5,12,13, we use a gonad-less mutant to focus the analysis on protein insolubility in non-reproductive tissues. The method presented enables the analysis of highly-insoluble, large aggregates that are insoluble in 0.5% SDS and pelleted by relatively low centrifugal speed. Alternatively, a less stringent extraction protocol to collect also smaller and more soluble aggregates has been published elsewhere10. In addition, we describe the method used to assess aggregation in vivo in C. elegans.
Overall, these methods in combination with RNA interference (RNAi) can evaluate the role of a gene of interest in modulating age-dependent protein aggregation. For this we describe the analysis of extracts from young and aged worms with and without knockdown of a specific protein of interest using RNAi. These methods should be a powerful tool to determine which components of the proteostasis network regulate protein insolubility. Several interventions such as reduced insulin/insulin-like growth factor (IGF) 1 signaling (IIS) have been shown to dramatically delay C. elegans aging14. Longevity pathways often induce protein-quality control mechanisms and thus these pathways could be actively influencing the rate of protein aggregation. As an example, we demonstrate reduced inherent protein aggregation in long-lived animals upon inhibition of the IIS pathway7.

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			<td class="xl18" height="40" style="width:161pt;height:30.0pt" width="215">Sequencing Grade Modified Trypsin</td>
			<td class="xl18" style="width:92pt" width="122">Promega</td>
			<td class="xl25" style="width:258pt" width="344">V5111</td>
			<td class="xl18" style="width:125pt" width="166"></td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl18" height="40" style="width:161pt;height:30.0pt" width="215">Isobaric tags for relative and absolute quantitation</td>
			<td class="xl18" style="width:92pt" width="122">Sciex</td>
			<td class="xl19">4352135</td>
			<td class="xl18" style="width:125pt" width="166">iTRAQ Reagents Multiplex Kit</td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl17" height="40" style="height:30.0pt">Centrifuge Avanti J-26XP</td>
			<td class="xl18" style="width:92pt" width="122">Beckmann Coulter</td>
			<td class="xl19">393126</td>
			<td class="xl17"></td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl17" height="40" style="height:30.0pt">Ultracentrifuge Optima Max-XP</td>
			<td class="xl18" style="width:92pt" width="122">Beckmann Coulter</td>
			<td class="xl19">393315</td>
			<td class="xl17"></td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl17" height="40" style="height:30.0pt">Centrifuge 5424R</td>
			<td class="xl18" style="width:92pt" width="122">Eppendorf</td>
			<td class="xl19">5404000413</td>
			<td class="xl17"></td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl17" height="40" style="height:30.0pt">Centrifuge 5702</td>
			<td class="xl18" style="width:92pt" width="122">Eppendorf</td>
			<td class="xl19">5702000329</td>
			<td class="xl17"></td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl17" height="40" style="height:30.0pt">Centrifuge Megafuge 40R</td>
			<td class="xl18" style="width:92pt" width="122">Thermo Scientific</td>
			<td class="xl19">75004518</td>
			<td class="xl17"></td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl17" height="40" style="height:30.0pt">Concentrator Plus</td>
			<td class="xl18" style="width:92pt" width="122">Eppendorf</td>
			<td class="xl19">5305000304</td>
			<td class="xl17">Centrifugal evaporator</td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl18" height="40" style="width:161pt;height:30.0pt" width="215">Fluorescent stereo-microscope M165 FC&#160;</td>
			<td class="xl18" style="width:92pt" width="122">Leica</td>
			<td class="xl19"></td>
			<td class="xl18" style="width:125pt" width="166">With Planapo 2.0x objective</td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl17" height="40" style="height:30.0pt">Dissection microscope</td>
			<td class="xl18" style="width:92pt" width="122">Leica&#160;</td>
			<td class="xl19"></td>
			<td class="xl17">Leica S6E</td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl18" height="80" rowspan="2" style="width:161pt;height:60.0pt" width="215">High magnification microscope Zeiss Axio Observer Z1</td>
			<td class="xl18" height="80" rowspan="2" style="width:92pt;height:60.0pt" width="122">Zeiss</td>
			<td class="xl19" height="80" rowspan="2" style="width:258pt;height:60.0pt" width="344"></td>
			<td class="xl16" height="80" rowspan="2" style="width:125pt;height:60.0pt" width="166">With PlanAPOCHROMAT 20x objective and Zeiss Axio Cam MRm</td>
		</tr>
		<tr height="40" style="height:30.0pt">
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl32" height="40" style="height:30.0pt">Software</td>
			<td class="xl33" style="width:92pt" width="122"></td>
			<td class="xl32"></td>
			<td class="xl17"></td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl17" height="40" style="height:30.0pt">Image analysis software</td>
			<td class="xl18" style="width:92pt" width="122">ImageJ</td>
			<td class="xl19"></td>
			<td class="xl17"></td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl18" height="40" style="width:161pt;height:30.0pt" width="215">Analysis of mass spectrometry data</td>
			<td class="xl18" style="width:92pt" width="122">Protein Prospector</td>
			<td class="xl136" style="width:258pt" width="344"></td>
			<td class="xl137">http://prospector.ucsf.edu/prospector/mshome.htm</td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl32" height="40" style="height:30.0pt">E.coli strain</td>
			<td class="xl33" style="width:92pt" width="122"></td>
			<td class="xl19"></td>
			<td class="xl17"></td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl17" height="40" style="height:30.0pt">OP50</td>
			<td class="xl18" style="width:92pt" width="122">CGC</td>
			<td class="xl19"></td>
			<td class="xl17"></td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl32" height="40" style="height:30.0pt">RNAi bacteria</td>
			<td class="xl33" style="width:92pt" width="122"></td>
			<td class="xl19"></td>
			<td class="xl17"></td>
		</tr>
		<tr height="40" style="height:30.0pt">
			<td class="xl17" height="40" style="height:30.0pt">L4440</td>
			<td class="xl18" style="width:92pt" width="122">Julie Ahringer RNAi library</td>
			<td class="xl19"></td>
			<td class="xl17"></td>
		</tr>
		<tr height="21" style="height:15.75pt">
			<td class="xl32" height="42" rowspan="2" style="width:161pt;height:31.5pt" width="215">C. elegans mutants</td>
			<td class="xl33" height="42" rowspan="2" style="width:92pt;height:31.5pt" width="122"></td>
			<td class="xl32" height="42" rowspan="2" style="width:258pt;height:31.5pt" width="344"></td>
			<td class="xl19" height="42" rowspan="2" style="width:125pt;height:31.5pt" width="166"></td>
		</tr>
		<tr height="21" style="height:15.75pt">
		</tr>
		<tr height="42" style="height:31.5pt">
			<td class="xl17" height="42" style="height:31.5pt">CF2253</td>
			<td class="xl18" style="width:92pt" width="122">CGC, strain name: EJ1158&#160;</td>
			<td class="xl40" style="width:258pt" width="344"></td>
			<td class="xl17">Genotype: gon-2(q388)</td>
		</tr>
		<tr height="21" style="height:15.75pt">
			<td class="xl33" height="42" rowspan="2" style="width:161pt;height:31.5pt" width="215">C. elegans transgenics</td>
			<td class="xl33" height="42" rowspan="2" style="width:92pt;height:31.5pt" width="122"></td>
			<td class="xl32" height="42" rowspan="2" style="width:258pt;height:31.5pt" width="344"></td>
			<td class="xl19" height="42" rowspan="2" style="width:125pt;height:31.5pt" width="166"></td>
		</tr>
		<tr height="21" style="height:15.75pt">
		</tr>
		<tr height="21" style="height:15.75pt">
			<td class="xl18" height="42" rowspan="2" style="width:161pt;height:31.5pt" width="215">DCD214</td>
			<td class="xl25" height="42" rowspan="2" style="width:92pt;height:31.5pt" width="122">Della David&#39;s lab at DZNE T&#252;bingen</td>
			<td class="xl40" height="42" rowspan="2" style="width:258pt;height:31.5pt" width="344"></td>
			<td class="xl68" height="42" rowspan="2" style="width:125pt;height:31.5pt" width="166">Genotype: N2; uqIs24[Pmyo-2::tagrfp::pab-1]</td>
		</tr>
		<tr height="21" style="height:15.75pt">
		</tr>
		<tr height="21" style="height:15.75pt">
			<td class="xl17" height="42" rowspan="2" style="width:161pt;height:31.5pt" width="215">DCD215</td>
			<td class="xl87" height="42" rowspan="2" style="width:92pt;height:31.5pt" width="122">Della David&#39;s lab at DZNE T&#252;bingen</td>
			<td class="xl40" height="42" rowspan="2" style="width:258pt;height:31.5pt" width="344"></td>
			<td class="xl68" height="42" rowspan="2" style="width:125pt;height:31.5pt" width="166">Genotype: daf-2(e1370) III; uqIs24[Pmyo-2::tagrfp::pab-1]</td>
		</tr>
		<tr height="21" style="height:15.75pt">
		</tr>
	</tbody>
</table>

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.

We used the methods presented here to evaluate how long-lived animals with reduced IIS modulate age-dependent protein aggregation. By Western blot (see step 2.2, Quick insoluble protein extraction for Western blot analysis), we analyzed the total and the insoluble protein content of young (day 3 of adulthood) and aged (day 18 of adulthood) worms on control RNAi and on RNAi targeting the insulin/IGF-1-like receptor daf-2. We observed no large changes in total protein levels with a...

Watch this Scientific Journal Video about Methods to Study Changes in Inherent Protein Aggregation with Age in Caenorhabditis elegans at JoVE.com

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.

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 ...

The overall goal of this experiment is to detect changes in protein insolubility with age in C.elegans and to evaluate how targeted gene knockdown influences this aging marker. This method can help answer key questions in the field of aging and proteostasis such as why organisms fail to maintain a healthy proteome with age. The main advantage of this technique is the opportunity to study protein aggregation during normal aging in the absence of disease processes.Though this method can provide insight into protein aggregation in C.elegans, it can also be adapted to other model organisms, for example to study age-related protein insolubility in mouse. To begin treatment, add 207.45 milliliters of S Basal media with additional reagents as described in the accompanying text protocol to a 2, 800 milliliter Fernbach culture flask. Add a final concentration of 50 micrograms per milliliter of Carbenicillin and one millimolar of IPTG and close the flask with a membrane screw cap.Take the L1's out of the 25 degree Celsius incubator and transfer them to 15 milliliter tubes. Centrifuge the L1's at 1, 900 times g for three minutes. After spinning, remove the supernatant.Under a microscope, count the L1's per two microliters and average the numbers obtained from at least nine drops. Next, add 50, 000 worms for the young worm collection and 100, 000 worms for the aged worm collection into four Fernbach culture flasks prepared in the previous step. Then, add control RNAi bacteria and RNAi bacteria for the gene of interest proportionally to the number of worms.After adding bacteria, complete worm culture with S Basal to bring the total volume to 300 milliliters. Incubate the worm culture at 25 degrees Celsius in a shaking incubator with 150 rpm until collection. Collect young worms at day two or three to measure basal levels of protein solubility.Pour the worms from one flask into a separation funnel and let the worms sediment for 10 minutes at room temperature. After the worms sediment, open the stop cock and drip the worms into one 50 milliliter tube. Next, split the worm pellet into two 15 milliliter tubes.Fill up the tubes to 15 milliliters with M9 and centrifuge the worms. To wash the worms, remove the supernatant and fill the tube up to 15 milliliters with M9.Repeat the centrifugation. Once washing is complete, transfer the worms to two 50 milliliter tubes and use ice cold M9 to fill up the total volume to 20 milliliters.To remove bacteria and dead worms, add the two 20 milliliter diluted worm pellets to two 50 milliliter tubes filled with 20 milliliters of ice cold 60%sucrose. Quickly centrifuge the tubes. With a 25 milliliter pipette, carefully remove up to 15 milliliters of the top worm layer.Place the top worm layer directly into 37 milliliters of M9 plus octoxynol-9 prepared on ice. Then, centrifuge the tubes at 2, 700 times g for three minutes at four degrees Celsius acceleration nine and deceleration seven. After discarding the supernatant, transfer the pellet into four 15 milliliter tubes and wash them twice with ice cold M9 plus octoxynol-9.Then, centrifuge the tubes. Remove the supernatant and fill the tubes up to the 15 milliliter mark with ice cold M9 plus octoxynol-9. Wash the worms with ice cold M9 and combine the four tubes into two tubes.Fill up the tubes to 15 milliliters and centrifuge. Remove the supernatant, fill up the two tubes with M9 at room temperature to a total volume of four milliliters and rotate them on a nutating mixer at 25 degrees Celsius for 40 minutes. After nutating, wash the worms twice with ice cold M9 plus octoxynol-9.Then, wash them twice with M9 and transfer the worms to one tube. Wash the worms in the reassembly or RAB high salt extraction buffer without inhibitors before collection. Remove the supernatant until there is no liquid on top of the worm pellet.Then, estimate the volume of the worm pellet and add an identical volume of RAB with inhibitors. Prepare a 50 milliliter tube half filled with liquid nitrogen on dry ice and using a Pasteur pipette, draw up the worms and slowly drip them into the tube. Allow the liquid nitrogen to evaporate and store the frozen worms at minus 80 degrees Celsius until further processing.Cool down the mortar with liquid nitrogen and perform the animal disruption on dry ice. Transfer the frozen worms to the pre-cooled mortar and grind them for 2.5 minutes. Add 100 milliliters of liquid nitrogen to the powder and grind for another 2.5 minutes.Use a microscope to check that the worm bodies are broken into small pieces. Then, transfer the powder into two milliliter tubes and store them at minus 80 degrees Celsius. On dry ice, weigh out two times 350 milligrams of ground worms per time point and per RNAi bacteria into two milliliter tubes.To remove the high salt soluble proteins, add two volumes per weight of already prepared RAB with inhibitors, one millimolar PMSF, 200 units per milliliter DNase I, and 100 micrograms per milliliter RNase A to each tube and solubilize the powder on ice. Draw up the suspension into a one milliliter syringe 15 times and incubate it on ice for 10 minutes. Centrifuge at 18, 400 times g for 20 minutes at four degrees Celsius.Go through the fat layer and collect the supernatant containing high salt soluble proteins into one two milliliter tube per condition. Remove the fat and discard it. Aliquot high salt soluble proteins to freeze at minus 80 degrees Celsius.To discard lipids, solubilize the pellet with 700 microliters of RAB with inhibitors containing one molar sucrose without DNase I and RNase A.Draw up the suspension into a syringe 10 times and incubate it on ice for five minutes. Be sure to remove all of the supernatant and lipids and discard them. To remove SDS-soluble proteins, solubilize the pellet with 700 microliters of RIPA buffer.Draw up the suspension into a syringe 10 times and incubate it for 10 minutes on ice. Centrifuge at 18, 400 g for 20 minutes at four degrees Celsius. Collect the supernatant containing SDS-soluble proteins and aliquot for freezing at minus 80 degrees Celsius.Pool two samples of each condition together after solubilizing each pellet with 500 microliters of RIPA buffer and draw up the suspension into a syringe 10 times. Be careful to remove all of the supernatant and discard it. Solubilize the final pellet containing highly insoluble proteins with 400 microliters 70%formic acid and draw up the suspension into a syringe 20 times.Incubate the suspension for 20 minutes on ice. Centrifuge the suspension in ultracentrifuge tubes to remove worm cuticle debris. Collect the supernatant that contains highly insoluble proteins and freeze it at minus 80 degrees Celsius.Total protein staining of insoluble protein content of young and aged worms revealed a strong age-related increase in highly insoluble protein levels in control animals and not in long lived animals. Antibody staining of PAB-1, an RNA binding protein with a predicted prion-like domain, confirmed mass spectrometry data that long lived animals maintained PAB-1 soluble with age. In vivo analysis was performed of transgenic animals expressing tagRFP PAB-1 in the pharyngeal muscles.In young animals, tagRFP PAB-1 was mainly diffusely located throughout the pharynx. With age, a progressive accumulation in bright puncta starting in the posterior pharyngeal bulb. During aging, we also observed aggregation in the anterior pharyngeal bulb in an increasing number of animals.Quantification of different tagRFP PAB-1 aggregation levels with age in wild type and daf-2 mutant background reveals strongly delayed tagRFP PAB-1 aggregation with age in long lived animals. After watching this video, you should have a good understanding of how to collect a large number of worms for protein extraction and how to isolate highly insoluble large aggregates for further analysis by mass spectrometry or SDS page.

methods-to-study-changes-inherent-protein-aggregation-with-age

Research

JoVE Journal

Biology

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 ...

4D Imaging of Protein Aggregation in Live Cells

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

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

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

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, ...

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 ...

In Vitro Aggregation Assays Using Hyperphosphorylated Tau Protein

Alzheimer's disease is one of a large group of neurodegenerative disorders known as tauopathies that are manifested by the neuronal deposits of hyperphosphorylated tau protein in the form of neurofibrillary tangles (NFTs). The density of NFT correlates well with cognitive impairment and other neurodegenerative symptoms, thus prompting the endeavor of developing tau aggregation-based therapeutics. Thus far, however, tau aggregation assays use recombinant or synthetic tau that is devoid of the pathology-related phosphorylation marks. Here we describe two assays using recombinant, hyperphosphorylated tau as the subject. These assays can be scaled up for high-throughput screens for compounds that can modulate the kinetics or stability of hyperphosphorylated tau aggregates. Novel therapeutics for Alzheimer's disease and other tauopathies can potentially be discovered using hyperphosphorylated tau isoforms.

In Vitro Aggregation Assays Using Hyperphosphorylated Tau Protein

Unmodified and hyperphosphorylated tau proteins were used in two in vitro aggregation assays to reveal the hyperphosphorylation-dependent fast aggregation kinetics. These assays pave the way for future screens for compounds that can modulate the propensity of hyperphosphorylated tau to form fibrils that underlie the progression of Alzheimer&#8217;s disease.

Alzheimer's disease is one of a large group of neurodegenerative disorders known as tauopathies that are manifested by the neuronal deposits of ...

Methods to Assess Subcellular Compartments of Muscle in C. elegans

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

Methods to Assess Subcellular Compartments of Muscle in C. elegans

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

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

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 ...

Combined Nucleotide and Protein Extractions in Caenorhabditis elegans

A single biological sample holds a plethora of information, and it is now common practice to simultaneously investigate several macromolecules to capture a full picture of the multiple levels of molecular processing and changes between different conditions. This protocol presents the method of isolating DNA, RNA, and protein from the same sample of the nematode Caenorhabditis elegans to remove the variation introduced when these biomolecules are isolated from replicates of similarly treated but ultimately different samples. Nucleic acids and protein are extracted from the nematode using the acid guanidinium thiocyanate-phenol-chloroform extraction method, with subsequent precipitation, washing, and solubilization of each. We show the successful isolation of RNA, DNA, and protein from a single sample from three strains of nematode and HeLa cells, with better protein isolation results in adult animals. Additionally, guanidinium thiocyanate-phenol-chloroform-extracted protein from nematodes improves the resolution of larger proteins, with enhanced detectable levels as observed by immunoblotting, compared to the traditional RIPA extraction of protein.
The method presented here is useful when investigating samples using a multiomic approach, specifically for the exploration of the proteome and transcriptome. Techniques that simultaneously assess multiomics are appealing because molecular signaling underlying complex biological phenomena is thought to occur at complementary levels; however, it has become increasingly common to see that changes in mRNA levels do not always reflect the same change in protein levels and that the time of collection is relevant in the context of circadian regulations. This method removes any intersample variation when assaying different contents within the same sample (intrasample.)

Combined Nucleotide and Protein Extractions in Caenorhabditis elegans

Here, we present a protocol for the isolation of RNA, DNA, and protein from the same sample, in an effort to reduce variation, improve reproducibility, and facilitate interpretations.

A single biological sample holds a plethora of information, and it is now common practice to simultaneously investigate several macromolecules to capture ...

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 ...