Name: quantification of lipid abundance and evaluation of lipid distribution in caenorhabditis elegans by nile red and oil red o staining
Uploaded: 2018-03-05T14:00:00
Description: Watch this Scientific Journal Video about Quantification of Lipid Abundance and Evaluation of Lipid Distribution in Caenorhabditis elegans by Nile Red and Oil Red O Staining at JoVE.com

This work was made possible by the NIH grant: R01GM109028 (S.P.C.)

1. Nile Red (NR) Staining of Lipids
<ol>
	<li>Preparation of 5 mg/mL NR stock solution
	<ol>
		<li>In a 500 mL bottle, add 100 mg of NR powder to 200 mL of 100% acetone.</li>
		<li>Cover the bottle with aluminum foil to avoid any exposure to light.</li>
		<li>Before use, stir the solution for 2 h in the dark.</li>
		<li>For long term use, store the NR stock solution in a tightly sealed bottle without any light exposure. Scale NR stock solution according to research needs. Ensure that the same stock solution is used acr...

<ol>
	<li>Greenspan, P., Mayer, E. P., Fowler, S. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nile+red:+a+selective+fluorescent+stain+for+intracellular+lipid+droplets.">Nile red: a selective fluorescent stain for intracellular lipid droplets.</a> J Cell Biol. 100 (3), 965-973 (1985).</li><li>Guo, Y., Cordes, K. R., Farese, R. V., Walther, T. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lipid+droplets+at+a+glance.">Lipid droplets at a glance.</a> J Cell Sci. 122 (6), 749-752 (2009).</li><li>Horobin, R. W., Kiernan, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Conn's biological stains: a handbook of dyes, stains and fluorochromes for use in biology and medicine. , (2002).</li><li>Hulme, S. E., Whitesides, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemistry+and+the+worm:+Caenorhabditis+elegans+as+a+platform+for+integrating+chemical+and+biological+research.">Chemistry and the worm: Caenorhabditis elegans as a platform for integrating chemical and biological research.</a> Angew Chem Int Edit. 50 (21), 4774-4807 (2011).</li><li>Khanna, A., Johnson, D. L., Curran, S. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Physiological+roles+for+mafr-1+in+reproduction+and+lipid+homeostasis.">Physiological roles for mafr-1 in reproduction and lipid homeostasis.</a> Cell Rep. 9 (6), 2180-2191 (2014).</li><li>Lynn, D. A., Dalton, H. M., Sowa, J. N., Wang, M. C., Soukas, A. A., Curran, S. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Omega-3+and-6+fatty+acids+allocate+somatic+and+germline+lipids+to+ensure+fitness+during+nutrient+and+oxidative+stress+in+Caenorhabditis+elegans.">Omega-3 and-6 fatty acids allocate somatic and germline lipids to ensure fitness during nutrient and oxidative stress in Caenorhabditis elegans.</a> P Natl Acad Sci USA. 112 (50), 15378-15383 (2015).</li><li>Pang, S., Lynn, D. A., Lo, J. Y., Paek, J., Curran, S. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SKN-1+and+Nrf2+couples+proline+catabolism+with+lipid+metabolism+during+nutrient+deprivation.">SKN-1 and Nrf2 couples proline catabolism with lipid metabolism during nutrient deprivation.</a> Nat Commun. 5, (2014).</li><li>Saltiel, A. R., Kahn, C. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Insulin+signalling+and+the+regulation+of+glucose+and+lipid+metabolism.">Insulin signalling and the regulation of glucose and lipid metabolism.</a> Nature. 414 (6865), 799-806 (2001).</li><li>Witting, M., Schmitt-Kopplin, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Caenorhabditis+elegans+lipidome:+A+primer+for+lipid+analysis+in+Caenorhabditis+elegans.">The Caenorhabditis elegans lipidome: A primer for lipid analysis in Caenorhabditis elegans.</a> Arch Biochem Biophys. 589, 27-37 (2016).</li><li>Yen, K., Le, T. T., Bansal, A., Narasimhan, S. D., Cheng, J. X., Tissenbaum, H. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comparative+study+of+fat+storage+quantitation+in+nematode+Caenorhabditis+elegans+using+label+and+label-free+methods.">A comparative study of fat storage quantitation in nematode Caenorhabditis elegans using label and label-free methods.</a> PloS One. 5 (9), e12810 (2010).</li><li>Zhang, Y., Zou, X., Ding, Y., Wang, H., Wu, X., Liang, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparative+genomics+and+functional+study+of+lipid+metabolic+genes+in+Caenorhabditis+elegans.">Comparative genomics and functional study of lipid metabolic genes in Caenorhabditis elegans.</a> BMC Genomics. 14 (1), 164 (2013).</li><li>Folick, A., Min, W., Wang, M. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Label-free+imaging+of+lipid+dynamics+using+Coherent+Anti-stokes+Raman+Scattering+(CARS)+and+Stimulated+Raman+Scattering+(SRS)+microscopy.">Label-free imaging of lipid dynamics using Coherent Anti-stokes Raman Scattering (CARS) and Stimulated Raman Scattering (SRS) microscopy.</a> Curr Opin Genet Dev. 21 (5), 585-590 (2011).</li><li>Pino, E. C., Webster, C. M., Carr, C. E., Soukas, A. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biochemical+and+high+throughput+microscopic+assessment+of+fat+mass+in+Caenorhabditis+elegans.">Biochemical and high throughput microscopic assessment of fat mass in Caenorhabditis elegans.</a> J Vis Exp. (73), (2013).</li><li>O'Rourke, E. J., Soukas, A. A., Carr, C. E., Ruvkun, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=C.+elegans+major+fats+are+stored+in+vesicles+distinct+from+lysosome-related+organelles.">C. elegans major fats are stored in vesicles distinct from lysosome-related organelles.</a> Cell Metab. 10 (5), 430-435 (2009).</li></ol>

The rise in obesity and metabolic disease rates makes C. elegans a suitable model to study the mechanisms that regulate fat accumulation in cells and tissues. Recent evidence suggests that the changes in lipid levels are correlated with cellular processes ranging from insulin signaling8, the activation of hormone receptors2, to reproductive output5. Compared to label-free microscopy and chromatography methods, Nile red and oil red O are rela...

Lipids are essential for life. They are integral components of membranes, act as secondary messengers and signal transducers, and have crucial functions in energy storage. When lipid metabolism is dysregulated, it leads to diseases like obesity and type II diabetes, which are pressing public health concerns9. Caenorhabditis elegans (C. elegans) is an excellent model organism in which to study lipid metabolism because it has a relatively short life cycle, a transparent body, a known cell lineage, and a fully sequenced genome. Primarily a hermaphrodite, C. elegans allows researchers to raise large numbers of isogenic animals in short periods of time to carryout high-throughput forward genetic screens to study a wide array of metabolic genes and pathways4. This approach has revealed a high degree of conservation in 273 C. elegans lipid metabolism genes among humans, mice, rats and drosophila. Furthermore, over 300 lipid genes in C. elegans have human orthologues that are associated with diseases unrelated to metabolic syndrome11. Traditionally, examination of lipid storage in C. elegans has mostly relied on dye-labeled assays, which provide robust information about lipid accumulation. Less common is a description of where lipids localize and measured differences in lipid abundance across tissues. However, recent work has revealed that lipid distribution can be as important as lipid accumulation6.
Lately, studies have begun integrating methods such as high performance liquid chromatography-mass spectrometry (HPLC-MS), gas chromatography-mass spectrometry (GC-MS), and coherent anti-stokes Raman scattering (CARS) microscopy to address the shortcomings of stain-based approaches by directly analyzing the contents of lipid extracts, specific lipid fractions, and lipid deposits, respectively10,11. Moreover, CARS microscopy has revealed that Nile red can only serve as a proxy for fat accumulation when used as a fixative dye, for its use as a vital stain leads to off-target staining of auto-fluorescent organelles10. However, the required technical expertise and costs associated with these chromatography and microscopy methods make their use untenable for many research questions. In this article, we discuss a convenient and reliable method to fixate and stain neutral lipid deposits in C. elegans using Nile red and oil red O to distinguish lipid abundance in whole animals and in specific tissues.
Nile red, 9-diethylamino-5H-benzo[&#945;]phenoxazine-5-one, is a benzophenoxazone dye that readily dissolves in various organic solvents, but is mostly insoluble in water. It is an excellent lysochrome dye used to stain neutral lipids such as triglycerides or cholesterol esters because it features a strong color, solubilizes well in lipids, has negligible interaction with surrounding tissues, and is less soluble in the solvent than in lipids. It has an excitation and emission maxima of 450-500 and 520 nm, respectively1. When Nile red-stained C. elegans is viewed for green fluorescence, discrete lipid bodies can be observed throughout the intestine and other tissues either in clusters or evenly dispersed, depending on the animal&#39;s genotype or experimental treatment7.
Oil red O is a lysochrome, fat-soluble dye used to stain triglycerides and lipoproteins. It is called an azo dye because its chemical structure contains two azo groups attached to three aromatic rings. It is difficult to ionize, which renders it highly soluble in lipids. Its stain color is red and its light absorption maximum is 518 nm 3. C. elegans stained with oil red O show red lipid droplets that stand out against the animal&#39;s transparent body, which facilitates qualitative assessment of lipid distribution among different tissues6.

<table>
	<tbody>
		<tr>
			<td>Imager.M2m Microscope</td>
			<td>Zeiss</td>
			<td>n/a</td>
			<td>Fluorescence microscope</td>
		</tr>
		<tr>
			<td>ERC5s camera</td>
			<td>Axiocam</td>
			<td>n/a</td>
			<td>Color-capable</td>
		</tr>
		<tr>
			<td>MRm camera</td>
			<td>Axiocam</td>
			<td>n/a</td>
			<td>Fluorescence-capable</td>
		</tr>
		<tr>
			<td>Nile red</td>
			<td>Thermo Fisher</td>
			<td>N1142</td>
			<td>Lipid Stain</td>
		</tr>
		<tr>
			<td>Oil red O</td>
			<td>Alfa Aesar</td>
			<td>A12989</td>
			<td>Lipid Stain</td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>Thermo Fisher</td>
			<td>D1306</td>
			<td>DNA stain</td>
		</tr>
		<tr>
			<td>Isopropyl Alcohol</td>
			<td>BDH</td>
			<td>BDH1133-1LP</td>
			<td>Fixative solution</td>
		</tr>
		<tr>
			<td>0.2 &#181;m seterile syringe filter</td>
			<td>VWR</td>
			<td>28145-477</td>
			<td>Cellulose acetate filter</td>
		</tr>
		<tr>
			<td>Centrifuge 5430</td>
			<td>Eppendorf</td>
			<td>5428000015</td>
			<td>Centrifuge</td>
		</tr>
		<tr>
			<td>Shaker Rotisserie</td>
			<td>Lab Quake</td>
			<td>400110Q</td>
			<td>Shaker</td>
		</tr>
		<tr>
			<td>Tube Rotator</td>
			<td>VWR</td>
			<td>10136-084</td>
			<td>Rotator</td>
		</tr>
		<tr>
			<td>K2HPO4</td>
			<td>Sigma-Aldrich</td>
			<td>7758-11-4</td>
			<td>NGM</td>
		</tr>
		<tr>
			<td>KH2PO4</td>
			<td>Sigma-Aldrich</td>
			<td>7778-77-0</td>
			<td>NGM</td>
		</tr>
		<tr>
			<td>MgSO4</td>
			<td>Alfa Aesar</td>
			<td>7786-30-3</td>
			<td>NGM</td>
		</tr>
		<tr>
			<td>CaCl2</td>
			<td>Sigma-Aldrich</td>
			<td>10035-04-8</td>
			<td>NGM</td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Sigma-Aldrich</td>
			<td>7647-14-5</td>
			<td>NGM</td>
		</tr>
		<tr>
			<td>Cholesterol</td>
			<td>Sigma-Aldrich</td>
			<td>57-88-5</td>
			<td>NGM</td>
		</tr>
		<tr>
			<td>Peptone</td>
			<td>BD Biosciences</td>
			<td>211677</td>
			<td>NGM</td>
		</tr>
		<tr>
			<td>Agar</td>
			<td>Teknova</td>
			<td>L9110</td>
			<td>NGM</td>
		</tr>
		<tr>
			<td>LB media</td>
			<td>Sigma-Aldrich</td>
			<td>L3147</td>
			<td>Bacterial growth</td>
		</tr>
	</tbody>
</table>

quantification of lipid abundance and evaluation of lipid distribution in caenorhabditis elegans by nile red and oil red o staining

Caenorhabditis elegans is an exceptional model organism in which to study lipid metabolism and energy homeostasis. Many of its lipid genes are conserved in humans and are associated with metabolic syndrome or other diseases. Examination of lipid accumulation in this organism can be carried out by fixative dyes or label-free methods. Fixative stains like Nile red and oil red O are inexpensive, reliable ways to quantitatively measure lipid levels and to qualitatively observe lipid distribution across tissues, respectively. Moreover, these stains allow for high-throughput screening of various lipid metabolism genes and pathways. Additionally, their hydrophobic nature facilitates lipid solubility, reduces interaction with surrounding tissues, and prevents dissociation into the solvent. Though these methods are effective at examining general lipid content, they do not provide detailed information about the chemical composition and diversity of lipid deposits. For these purposes, label-free methods such as GC-MS and CARS microscopy are better suited, their costs notwithstanding.

SKN-1 is a bZip, cytoprotective transcription factor that shares homology with mammalian NRF2 and has been shown to mediate fatty acid oxidation. Depending on the glucose concentration in their diet, worms with a constitutively activated skn-1 allele show different lipid levels when stained with Nile red7. Figure 1A-C shows activated skn-1 animals exposed to conditions that lead to increasing lipid le...

Watch this Scientific Journal Video about Quantification of Lipid Abundance and Evaluation of Lipid Distribution in Caenorhabditis elegans by Nile Red and Oil Red O Staining at JoVE.com

Quantification of Lipid Abundance and Evaluation of Lipid Distribution in Caenorhabditis elegans by Nile Red and Oil Red O Staining

Nile red staining of fixed Caenorhabditis elegans is a method for quantitative measurement of neutral lipid deposits, while oil red O staining facilitates qualitative assessment of lipid distribution among tissues.

Quantification of Lipid Abundance and Evaluation of Lipid Distribution in Caenorhabditis elegans by Nile Red and Oil Red O Staining

Caenorhabditis elegans is an exceptional model organism in which to study lipid metabolism and energy homeostasis. Many of its lipid genes are conserved ...

The overall goal of these staining methods is to quantify intracellular lipid abundance and evaluate lipid distribution among different tissues. This method can help answer key questions in lipid metabolism such as how are lipids genetically and biochemically regulated and which disease states this regulate lipid homeostasis. The main advantage of this technique is that it is relatively simple and inexpensive to carry out.To carry out Nile Red lipid staining, plate worms on Nematode Growth Medium or NGM seeded with late log OP50 E.coli and grow the worms at 20 degrees Celsius to early L4 stage. Wash the worms with one millimeter of PBST solution and transfer the worm suspension to a 1.5 milliliter microfuge tube. Centrifuge the worms at 560 times gravity for one minute.Then remove the supernatant and repeat the PBST wash until the E.coli is cleared from the suspension. Next, to the worm pellet, add 100 microliters of 40%isopropanol or 60%for ORO staining and incubate the sample at room temperature for three minutes. The addition of isopropanol is crucial for proper permeabilization of the worms before staining.Centrifuge the worms at 560 times gravity for one minute and remove the supernatant without disrupting the worm pellet. It is important to minimize light exposure during the centrifugation steps. Now while in the dark, add 600 microliters of previously prepared NR working solution to each sample.Invert the tubes three times and fully mix the worms and solution. Then incubate the sample in the dark at room temperature for two hours. Following incubation, centrifuge the worms and remove the supernatant.Then add 600 microliters of PBST and incubate the samples in the dark for 30 minutes to remove the excess NR stain. After spinning the samples again as before, remove all but approximately 50 microliters of supernatant and resuspend the worm pellet in the remaining solution. To prepare slides for imaging, pipette five microliters of worm suspension onto a microscope slide and carefully apply a coverslip to avoid trapping any air bubbles.Using the FITC GFP channel to image NR stained worms and trying different exposure times, image the worms at five-fold magnification to capture several animals per field of view. Then switch to 10-fold magnification for better quantification of individual worms. To quantify the images, upload the micrographs to ImageJ.In the image pull down menu, adjust the brightness, contrast of the image deck, and propagate changes to all the images by clicking apply. Use the polygon selection tool to delineate each imaged worm and under the analysis pull down menu, use the measure function to qualify fluorescence intensity emitted by NR.For each image, measure five background locations and calculate the average background fluorescence intensity. Add 600 microliters of Oil Red O or ORO working solution to each sample and invert the tube three times to mix the worms well and the ORO.Rotate the samples at 30 RPM and RT for two hours. Centrifuge the samples at 560 times gravity for one minute and aspirate all the supernatant except for 100 microliters. Then use 600 microliters of PBST to resuspend the samples and rotate the tubes at 30 RPM for 30 minutes to remove excess ORO staining.To better distinguish the location of the animals'germ line in the intestinal cells, stain nuclei by adding one microliter of DAPI for every one milliliter of ORO working solution. Then to prepare slides for imaging, resuspend the worms and the remaining supernatant and mix the solution well. Put five microliters of worm suspension on a microscope slide and carefully apply a coverslip ensuring that no air bubbles form.To image the ORO stained worms, use a color capable camera at five-fold magnification to image several worms in one field of view. Then switch to 10-fold magnification for better examination of individual worms. Finally, after uploading the images to ImageJ and creating an image deck according to the text protocol, categorize the images according to lipid accumulation throughout the animal's body or in specific tissues.SKN-1 shares homology with mammalian Nrf2 and has been shown to mediate fatty acid oxidation. This figure shows activated SKN-1 animals exposed to conditions that lead to increasing lipid levels. As seen in these images, NR fluorescence captured using the FITC GFP channel is prominent along the intestine, but is dimmer in the head, tail, and intestinal lumen.While it is easy to categorize the worms according to the presence or absence of Age-dependent Somatic Depletion of Fat or ASDF, it may be difficult to identify animals with intermediate fat loss. Compared to non-ASDF animals, which show bright red staining throughout the body with few translucent areas, ASDF worms exhibit noticeable fat depletion in intestinal cells. Animals in the process of developing ASDF often show translucent spots where most of the fat loss eventually occur.Moreover, ASDF worms may still feature bright red staining in the head and tail regions because the phenotype is not defined by complete somatic fat loss, but by extensive fat depletion relative to non-aged animals. Once mastered, this technique can be done in three hours plus imaging time if it is performed properly. While attempting this procedure, it's important to remember to wash and permeabilize worms no more than 30 minutes before staining.Following this procedure, other methods like CARS microscopy can be performed to compare the type of lipid species each technology identifies and to determine which method is better suited for specific types of questions. After watching this video, you should have a good understanding of how to quantify lipids and evaluate lipid distribution in the worms using Nile Red and Oil Red O staining, followed by ImageJ micrograph analysis.

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Research

JoVE Journal

Biology

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 ...

Detecting Protein Subcellular Localization by Green Fluorescence Protein Tagging and 4',6-Diamidino-2-phenylindole Staining in Caenorhabditis elegans

In this protocol, a green fluorescence protein (GFP) fusion protein and 4',6-diamidino-2-phenylindole (DAPI) staining are used to track protein subcellular localization changes; in particular, a nuclear translocation under a heat stress condition. Proteins react correspondingly to external and internal signals. A common mechanism is to change its subcellular localization. This article describes a protocol to track protein localization that does not require an antibody, radioactive labeling, or a confocal microscope. In this article, GFP is used to tag the target protein EXL-1 in C. elegans, a member of the chloride intracellular channel proteins (CLICs) family, including mammalian CLIC4. An integrated translational exl-1::gfp transgenic line (with a promoter and a full gene sequence) was created by transformation and &#947;-radiation, and stably expresses the gene and gfp. Recent research showed that upon heat stress, not oxidative stress, EXL-1::GFP accumulates in the nucleus. Overlapping the GFP signal with both the nuclei structure and the DAPI signals confirms the EXL-1 subcellular localization changes under stress. This protocol presents two different fixation methods for DAPI staining: ethanol fixation and acetone fixation. The DAPI staining protocol presented in this article is fast and efficient and preserves both the GFP signal and the protein subcellular localization changes. This method only requires a fluorescence microscope with Nomarski, a FITC filter, and a DAPI filter. It is suitable for a small laboratory setting, undergraduate student research, high school student research, and biotechnology classrooms.

Detecting Protein Subcellular Localization by Green Fluorescence Protein Tagging and 4',6-Diamidino-2-phenylindole Staining in Caenorhabditis elegans

This protocol demonstrates how to track a protein nuclear translocation under heat stress by using a green fluorescence protein (GFP) fusion protein as a marker and 4',6-diamidino-2-phenylindole (DAPI) staining. The DAPI staining protocol is fast and preserves the GFP and protein subcellular localization signals.

In this protocol, a green fluorescence protein (GFP) fusion protein and 4',6-diamidino-2-phenylindole (DAPI) staining are used to track protein ...

Measurement of Energy Metabolism in Explanted Retinal Tissue Using Extracellular Flux Analysis

High acuity vision is a heavily energy-consuming process, and the retina has developed several unique adaptations to precisely meet such demands while maintaining transparency of the visual axis. Perturbations to this delicate balance cause blinding illnesses, such as diabetic retinopathy. Therefore, the understanding of energy metabolism changes in the retina during disease is imperative to the development of rational therapies for various causes of vison loss. The recent advent of commercially-available extracellular flux analyzers has made the study of retinal energy metabolism more accessible. This protocol describes the use of such an analyzer to measure contributions to retinal energy supply through its two principle arms - oxidative phosphorylation and glycolysis - by quantifying changes in oxygen consumption rates (OCR) and extracellular acidification rates (ECAR) as proxies for these pathways. This technique is readily performed in explanted retinal tissue, facilitating assessment of responses to multiple pharmacologic agents in a single experiment. Metabolic signatures in retinas from animals lacking rod photoreceptor signaling are compared to wild-type controls using this method. A major limitation in this technique is the lack of ability to discriminate between light-adapted and dark-adapted energy utilization, an important physiologic consideration in retinal tissue.

This technique describes real time recording of oxygen consumption and extracellular acidification rates in explanted mouse retinal tissues using an extracellular flux analyzer.

High acuity vision is a heavily energy-consuming process, and the retina has developed several unique adaptations to precisely meet such demands while ...

Dissection and Lipid Droplet Staining of Oenocytes in Drosophila Larvae

Lipids are essential for animal development and physiological homeostasis. Dysregulation of lipid metabolism results in various developmental defects and diseases, such as obesity and fatty liver. Usually, lipids are stored in lipid droplets, which are the multifunctional lipid storage organelles in cells. Lipid droplets vary in size and number in different tissues and under different conditions. It has been reported that lipid droplets are tightly controlled through regulation of its biogenesis and degradation. In Drosophila melanogaster, the oenocyte is an important tissue for lipid metabolism and has been recently identified as a human liver analogue regarding lipid mobilization in response to stress. However, the mechanisms underlying the regulation of lipid droplet metabolism in oenocytes remain elusive. To solve this problem, it is of utmost importance to develop a reliable and sensitive method to directly visualize lipid droplet dynamic changes in oenocytes during development and under stressful conditions. Taking advantage of the lipophilic BODIPY 493/503, a lipid droplet-specific fluorescent dye, described here is a detailed protocol for the dissection and subsequent lipid droplet staining in the oenocytes of Drosophila larvae in response to starvation. This allows for qualitative analysis of lipid droplet dynamics under various conditions by confocal microscopy. Furthermore, this rapid and highly reproducible method can also be used in genetic screens for indentifying novel genetic factors involving lipid droplet metabolism in oenocytes and other tissues.

Dissection and Lipid Droplet Staining of Oenocytes in Drosophila Larvae

Presented here are detailed methods for the dissection and lipid droplet staining of oenocytes in Drosophila larvae using BODIPY 493/503, a lipid droplet-specific fluorescent dye.

Lipids are essential for animal development and physiological homeostasis. Dysregulation of lipid metabolism results in various developmental defects and ...

Isolation and Characterization of Adult Cardiac Fibroblasts and Myofibroblasts

Cardiac fibrosis in response to injury is a physiological response to wound healing. Efforts have been made to study and target fibroblast subtypes that mitigate fibrosis. However, fibroblast research has been hindered due to the lack of universally acceptable fibroblast markers to identify quiescent as well as activated fibroblasts. Fibroblasts are a heterogenous cell population, making them difficult to isolate and characterize. The presented protocol describes three different methods to enrich fibroblasts and myofibroblasts from uninjured and injured mouse hearts. Using a standard and reliable protocol to isolate fibroblasts will enable the study of their roles in homeostasis as well as fibrosis modulation.

Obtaining a pure population of fibroblasts is crucial to studying their role in wound repair and fibrosis. Described here is a detailed method to isolate fibroblasts and myofibroblasts from uninjured and injured mouse hearts followed by characterization of their purity and functionality by immunofluorescence, RTPCR, fluorescence-assisted cell sorting, and collagen gel contraction.

Cardiac fibrosis in response to injury is a physiological response to wound healing. Efforts have been made to study and target fibroblast subtypes that ...

Label-Free Imaging of Lipid Storage Dynamics in Caenorhabditis elegans using Stimulated Raman Scattering Microscopy

Lipid metabolism is a fundamental physiological process necessary for cellular and organism health. Dysregulation of lipid metabolism often elicits obesity and many associated diseases including cardiovascular disorders, type II diabetes, and cancer. To advance the current understanding of lipid metabolic regulation, quantitative methods to precisely measure in vivo lipid storage levels in time and space have become increasingly important and useful. Traditional approaches to analyze lipid storage are semi-quantitative for microscopic assessment or lacking spatio-temporal information for biochemical measurement. Stimulated Raman scattering (SRS) microscopy is a label-free chemical imaging technology that enables rapid and quantitative detection of lipids in live cells with a subcellular resolution. As the contrast is exploited from intrinsic molecular vibrations, SRS microscopy also permits four-dimensional tracking of lipids in live animals. In the last decade, SRS microscopy has been widely used for small molecule imaging in biomedical research and overcome the major limitations of conventional fluorescent staining and lipid extraction methods. In the laboratory, we have combined SRS microscopy with the genetic and biochemical tools available to the powerful model organism, Caenorhabditis elegans, to investigate the distribution and heterogeneity of lipid droplets across different cells and tissues and ultimately to discover novel conserved signaling pathways that modulate lipid metabolism. Here, we present the working principles and the detailed setup of the SRS microscope and provide methods for its use in quantifying lipid storage at distinct developmental timepoints of wild-type and insulin signaling deficient mutant C. elegans.

Label-Free Imaging of Lipid Storage Dynamics in Caenorhabditis elegans using Stimulated Raman Scattering Microscopy

Stimulated Raman scattering (SRS) microscopy allows selective, label-free imaging of specific chemical moieties and it has been effectively employed to image lipid molecules in vivo. Here, we provide a brief introduction to the principle of SRS microscopy and describe methods for its use in imaging lipid storage in Caenorhabditis elegans.

Lipid metabolism is a fundamental physiological process necessary for cellular and organism health. Dysregulation of lipid metabolism often elicits ...

Automating Aggregate Quantification in Caenorhabditis elegans

A rise in the prevalence of neurodegenerative protein conformational diseases (PCDs) has fostered a great interest in this subject over the years. This increased attention has called for the diversification and improvement of animal models capable of reproducing disease phenotypes observed in humans with PCDs. Though murine models have proven invaluable, they are expensive and are associated with laborious, low-throughput methods. Use of the Caenorhabditis elegans nematode model to study PCDs has been justified by its relative ease of maintenance, low cost, and rapid generation time, which allow for high-throughput applications. Additionally, high conservation between the C. elegans and human genomes makes this model an invaluable discovery tool. Nematodes that express fluorescently tagged tissue-specific polyglutamine (polyQ) tracts exhibit age- and polyQ length-dependent aggregation characterized by fluorescent foci. Such reporters are often employed as proxies to monitor changes in proteostasis across tissues. Manual aggregate quantification is time-consuming, limiting experimental throughput. Furthermore, manual foci quantification can introduce bias, as aggregate identification can be highly subjective. Herein, a protocol consisting of worm culturing, image acquisition, and data processing was standardized to support high-throughput aggregate quantification using C. elegans that express intestine-specific polyQ. By implementing a C. elegans-based image processing pipeline using CellProfiler, an image analysis software, this method has been optimized to separate and identify individual worms and enumerate their respective aggregates. Though the concept of automation is not entirely unique, the need to standardize such procedures for reproducibility, elimination of bias from manual counting, and increase throughput is high. It is anticipated that these methods can drastically simplify the screening process of large bacterial, genomic, or drug libraries using the C. elegans model.

Automating Aggregate Quantification in Caenorhabditis elegans

The following protocol describes the development and optimization of a high-throughput workflow for worm culturing, fluorescence imaging, and automated image processing to quantify polyglutamine aggregates as an assessment of changes in proteostasis.

A rise in the prevalence of neurodegenerative protein conformational diseases (PCDs) has fostered a great interest in this subject over the years. This ...

Lipid Supplementation for Longevity and Gene Transcriptional Analysis in Caenorhabditis elegans

Aging is a complex process characterized by progressive physiological changes resulting from both environmental and genetic contributions. Lipids are crucial in constituting structural components of cell membranes, storing energy, and as signaling molecules. Regulation of lipid metabolism and signaling is essential to activate distinct longevity pathways. The roundworm Caenorhabditis elegans is an excellent and powerful organism to dissect the contribution of lipid metabolism and signaling in longevity regulation. Multiple research studies have described how diet supplementation of specific lipid molecules can extend C. elegans lifespan; however, minor differences in the supplementation conditions can cause reproducibility issues among scientists in different labs. Here, two detailed supplementation methods for C. elegans are reported employing lipid supplementation either with bacteria seeded on plates or bacterial suspension in liquid culture. Also provided herein are the details to perform lifespan assays with lifelong lipid supplementation and qRT-PCR analysis using a whole worm lysate or dissected tissues derived from a few worms. Using a combination of longitudinal studies and transcriptional investigations upon lipid supplementation, the feeding assays provide dependable approaches to dissect how lipids influence longevity and healthy aging. This methodology can also be adapted for various nutritional screening approaches to assess changes in a subset of transcripts using either a small number of dissected tissues or a few animals.

Lipid Supplementation for Longevity and Gene Transcriptional Analysis in Caenorhabditis elegans

The present protocol describes lipid supplementation methods in liquid and on-plate cultures for Caenorhabditis elegans, coupled with longitudinal studies and gene transcriptional analysis from bulk or a few worms and worm tissues.

Aging is a complex process characterized by progressive physiological changes resulting from both environmental and genetic contributions. Lipids are ...

Live Cell Imaging of Lipid Droplet Size and Fusion Using Oil Red O and BODIPY

Evaluation of Lipid Droplet Size and Fusion in Bovine Hepatic Cells

Lipid droplets (LDs) are organelles that play an important role in lipid metabolism and neutral lipid storage in cells. They are associated with a variety of metabolic diseases, such as obesity, fatty liver disease, and diabetes. In hepatic cells, the sizes and numbers of LDs are signs of fatty liver disease. Moreover, the oxidative stress reaction, cell autophagy, and apoptosis are often accompanied by changes in the sizes and numbers of LDs. As a result, the dimensions and quantity of LDs are the basis of the current research regarding the mechanism of LD biogenesis. Here, in fatty acid-induced bovine hepatic cells, we describe how to use oil red O to stain LDs and to investigate the sizes and numbers of LDs. The size distribution of LDs is statistically analyzed. The process of small LDs fusing into large LDs is also observed by a live cell imaging system. The current work provides a way to directly observe the size change trend of LDs under different physiological conditions.

Author Spotlight: Evaluation of Lipid Droplet Size and Fusion in Bovine Hepatic Cells  

The present protocol describes how to use oil red O to dye lipid droplets (LDs), calculate the size and number of LDs in a fatty acid-induced fatty hepatocyte model, and use BODIPY 493/503 to observe the process of small LDs fusing into large LDs by live cell imaging.

Lipid droplets (LDs) are organelles that play an important role in lipid metabolism and neutral lipid storage in cells. They are associated with a variety ...

Application of Flow Vermimetry for Quantification and Analysis of the Caenorhabditis elegans Gut Microbiome

The composition of the gut microbiome can have a dramatic impact on host physiology throughout the development and the life of the animal. Measuring compositional changes in the microbiome is crucial in identifying the functional relationships between these physiological changes. Caenorhabditis elegans has emerged as a powerful host system to examine the molecular drivers of host-microbiome interactions. With its transparent body plan and fluorescent-tagged natural microbes, the relative levels of microbes within the gut microbiome of an individual C. elegans animal can be easily quantified using a large particle sorter. Here we describe the procedures for the experimental setup of a microbiome, collection, and analysis of C. elegans populations in the desired life stage, operation, and maintenance of the sorter, and statistical analyses of the resulting datasets. We also discuss considerations for optimizing sorter settings based on the microbes of interest, the development of effective gating strategies for C. elegans life stages, and how to utilize sorter capabilities to enrich animal populations based on gut microbiome composition. Examples of potential applications will be presented as part of the protocol, including the potential for scalability to high-throughput applications.

Application of Flow Vermimetry for Quantification and Analysis of the Caenorhabditis elegans Gut Microbiome

Caenorhabditis elegans is a powerful model to examine the molecular determinants driving host-microbiome interactions. We present a high throughput pipeline profiling the single animal levels of gut microbiome colonization together with key aspects of the C. elegans physiology.

The composition of the gut microbiome can have a dramatic impact on host physiology throughout the development and the life of the animal. Measuring ...