Name: antibody staining in c. elegans using &quot;freeze-cracking&quot;
Uploaded: 2013-10-14T21:15:00
Description: Watch this Scientific Journal Video about Antibody Staining in C. Elegans Using "Freeze-Cracking" at JoVE.com

Funding was provided by NSF CCLI#0633618 and Ohio University. Some strains were provided by the Caenorhabditis Genetics Center. Graduate student Reetobrata Basu appears in the video.

NOTE: Multiple protocol steps are presented with options for set-up and preparation depending on the specific conditions of the experiment. For these cases, alternative steps are presented as A, B, C, etc. The protocol with alternative steps is outlined in Figure 1.
1. Preparation of Polylysine Coated Slides
Three different types of slides may be used, depending upon the desired trade-off between ease of preparation, relative adhesion, and no...

<ol>
	<li>Harlow, E., Lane, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Antibodies: A Laboratory Manual. , (1988).</li><li>Mello, C., Fire, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+Transformation.">DNA Transformation.</a> Methods Cell Biol. 48, 451-482 (1995).</li><li>Boulin, T., Etchberger, J. F., Hobert, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reporter+gene+fusions.">Reporter gene fusions.</a> WormBook. , (2006).</li><li>Duerr, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immunohistochemistry.">Immunohistochemistry.</a> WormBook. , (2006).</li><li>Finney, M., 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=The+unc-86+gene+product+couples+cell+lineage+and+cell+identity+in+C.+elegans.">The unc-86 gene product couples cell lineage and cell identity in C. elegans.</a> Cell. 63, 895-905 (1990).</li><li>Garriga, G., Desai, C., Horvitz, H. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+interactions+control+the+direction+of+outgrowth,+branching+and+fasciculation+of+the+HSN+axons+of+Caenorhabditis+elegans.">Cell interactions control the direction of outgrowth, branching and fasciculation of the HSN axons of Caenorhabditis elegans.</a> Development. 117, 1071-1087 (1993).</li><li>Miller, D. M., Shakes, D. C., Epstein, H. F., Shakes, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immunofluorescence+microscopy.">Immunofluorescence microscopy.</a> Caenorhabditis elegans: Modern Biological Analysis of an Organism. , 365-394 (1995).</li><li>Crittenden, S. L., Troemel, E. R., Evans, T. C., Kimble, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GLP-1+is+localized+to+the+mitotic+region+of+the+C.+elegans+germ+line.">GLP-1 is localized to the mitotic region of the C. elegans germ line.</a> Development. 120, 2901-2911 (1994).</li><li>Strome, S., Wood, W. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immunofluorescence+visualization+of+germ-line-specific+cytoplasmic+granules+in+embryos,+larvae,+and+adults+of+Caenorhabditis+elegans.">Immunofluorescence visualization of germ-line-specific cytoplasmic granules in embryos, larvae, and adults of Caenorhabditis elegans.</a> Proc. Natl. Acad. Sci. U.S.A. 79, 1558-1562 (1982).</li><li>Albertson, D. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Formation+of+the+first+cleavage+spindle+in+nematode+embryos.">Formation of the first cleavage spindle in nematode embryos.</a> Dev. Biol. 101, 61-72 (1984).</li><li>Harlow, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Using Antibodies: A Laboratory Manual. , (1999).</li><li>Ahringer, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reverse+Genetics.">Reverse Genetics.</a> WormBook. , (2006).</li></ol>

The freeze-cracking protocol is one of several methods for antibody staining in C. elegans. It provides a relatively simple way to stain worms, but does require specific reagents and practice for optimum results. Critical steps (outlined in Figure 1) include: 1) slide preparation (see steps 1 and&#160;2) manual compression of the nematodes (see steps 2 and 3) rapid fixation (see step 3). First, to maximize adhesion of the nematodes to the slides, it is best to prepare slides with high molecular ...

To determine the cellular and subcellular localization of proteins, scientists have traditionally labeled tissues with antibodies selected to specifically recognize particular proteins1. In some model organisms such as C. elegans, antibody staining has often been replaced by molecular genetic techniques, which yield results more quickly. These include transforming organisms with constructs consisting of gene fusions between the promoter and coding regions of the gene of interest and green fluorescent protein. However, molecular techniques are subject to a number of artifacts, including problems with knowing the true promoter and changes in expression of constructs at high copy number (the usual techniques in C. elegans)2,3. Therefore, staining with antibodies remains a goal for many scientists studying protein function in vivo.
Staining tissues with antibodies can be difficult, since antibodies may only recognize their antigen in a particular conformation1. For example, antibodies may recognize only denatured or intact antigen fixed in a particular way and may not recognize the antigen in situ. The problem of antibody staining in nematodes is exacerbated by the fact that the cuticle of the nematode forms a relatively impermeable barrier, blocking access of antibodies to tissues.
There are several different methods used for antibody staining in C. elegans (reviewed in our previous work4). To stain intact &#39;worms,&#39; methods were developed to freeze and thaw in a relatively hard fixative (formaldehyde or glutaraldehyde); the freeze-thaw cycles help to crack the cuticle to allow rapid penetration of the fixative5. After fixation, the cuticle was permeabilized to allow penetration of the antibody; methods included treatment with reducing agents, collagenase, or both5-7. These treatments preserved morphology, but often reduced or destroyed antibody recognition. Alternative methods include dissection8 to allow antibody penetration.
&#34;Freeze-cracking&#34; is one way to gain access to the interior of the semi-intact worm to allow antibody staining9-10. Freeze-cracking can be performed with a variety of fixation conditions while avoiding collagenase and reduction treatments. The nematodes are placed between two adhesives slides, frozen, and then the slides are separated, leaving most of the nematode on the bottom slide and much of the cuticle on the top slide. The bottom slide can be placed in fixative and the entire slide with adhered nematodes is transferred through the antibody staining procedure. The method does present two major difficulties. First, it is difficult to apply the correct amount of pressure necessary to split the nematodes without seriously deforming them. Second, many of the worms will not stick to either slide, and will be lost in the fixative or rinses. However, with the proper slides and practice, the method will rapidly yield nematodes with reasonable morphology which can be used with a wide variety of fixatives and antibodies.
The method may be varied slightly, depending upon the goal of the experimenter. If staining of single nematodes is desired (e.g.&#160;to determine whether a single transformant has altered antibody staining), then slides with maximal adhesion (but higher background staining) can be used, such as laboratory-prepared slides with extra polylysine (see below). For formaldehyde or glutaraldehyde fixation, higher adhesion slides (laboratory-prepared polylysine slides) should be used, since nematodes adhere more poorly to polylysine after these fixations. If wild-type nematodes are being fixed with methanol and/or acetone, then slides with lower adhesion and lower background staining should be used (commercial or laboratory-prepared slides). If a variety of antibodies and fixatives are being used in the lab, a selection of slides may be prepared ahead of time and stored until needed.
After access to the nematode tissue has been gained, antibody staining procedures follow standard methods (with longer incubations characteristic of tissues rather than cells1,11).

<table border="1">
		<tbody>
		 <tr>
			<td>Name of Reagent/Material</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		 </tr>
		 <tr>
			<td>poly-L-lysine slide (ESCO brand)</td>
			<td>Fisher</td>
			<td>12-545-78</td>
			<td>Sigma brand slides also suitable</td>
		 </tr>
		 <tr>
			<td>poly-L-lysine hydrobromide</td>
			<td>Sigma</td>
			<td>P1524</td>
			<td>IMPORTANT: Brand and high molecular weight of polylysine critical</td>
		 </tr>
		 <tr>
			<td>single frosted edge slides</td>
			<td>Fisher</td>
			<td>48312-002</td>
			<td>Other brands are suitable</td>
		 </tr>
		 <tr>
			<td>sodium azide</td>
			<td>Sigma</td>
			<td>S2002-25G</td>
			<td>TOXIC, wear gloves and mask while weighing out powder to make 10% stock. Wear gloves when pipeting stock solution</td>
		 </tr>
		 <tr>
			<td>coplin staining jar</td>
			<td>VWR</td>
			<td>47751-792</td>
			<td>Other brands are suitable</td>
		 </tr>
		 <tr>
			<td>5-slide mailer</td>
			<td>Electron Microscopy Science</td>
			<td>71549-01</td>
			<td>One of many different brands of small slide holder, suitable for staining</td>
		 </tr>
		 <tr>
			<td>Paraformaldehyde</td>
			<td>VWR</td>
			<td>MK262159</td>
			<td>IMPORTANT: Regular formalin solutions (37% formaldehyde) are NOT suitable. Either 1) Dissolve crysatlaline paraformaldehyde in phosphate buffer and store in small aliquots frozen. Or 2) buy electron microscopy grade paraformaldehyde in aliquots. TOXIC -wear gloves; dispose of excess down sink with water.</td>
		 </tr>
		 <tr>
			<td>Glutaraldehyde solution, 25% in water</td>
			<td>Sigma</td>
			<td>G 5882</td>
			<td>IMPORTANT: purchase electron microscopy grade glutaraldehyde in ampules; TOXIC -wear gloves; dispose of excess down sink with water.</td>
		 </tr>
		 <tr>
			<td>Triton X-100</td>
			<td>VWR</td>
			<td>EM-9410</td>
			<td>Other brands are suitable</td>
		 </tr>
		 <tr>
			<td>Bovine Serum Albumin</td>
			<td>Fisher</td>
			<td>ICN820451</td>
			<td>Other brands are suitable</td>
		 </tr>
		 <tr>
			<td>Donkey Serum, lyophilized</td>
			<td>Jackson Immunoresearch</td>
			<td>017-000-121</td>
			<td>Other brands are suitable</td>
		 </tr>
		 <tr>
			<td>Cy3 Donkey anti-Mouse IgG multi-labeling</td>
			<td>Jackson Immunoresearch</td>
			<td>715-165-150</td>
			<td>This company is recommended for high quality multi-label (affinity depleted) antibodies. Select appropriate dye and antigen (animal used to raise primary antibody). </td>
		 </tr>
		 <tr>
			<td>n-propyl gallate</td>
			<td>Fisher</td>
			<td>ICN10274750</td>
			<td>Other brands are suitable</td>
		 </tr>
		 <tr>
			<td>DAPI, 4',6'-diamidino-2-phenylindole dihydrochloride</td>
			<td>Sigma</td>
			<td>D 9542</td>
			<td>TOXIC. Wear gloves and dispense into small aliquots and feeze to minimize exposure</td>
		 </tr>
		 <tr>
			<td>Whatman #1 15 cm diameter filters</td>
			<td>Fisher</td>
			<td>09805G</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Coverslip #1 1/2 rectangle 24 x 60 mm</td>
			<td>VWR</td>
			<td>48393-252</td>
			<td>#1 1/2 thickness is optically best</td>
		 </tr>
		 <tr>
			<td>Microscope slide folder</td>
			<td>VWR</td>
			<td>48429-092</td>
			<td>Other brands are suitable</td>
		 </tr>
		</tbody>
 </table>

antibody staining in c. elegans using &quot;freeze-cracking&quot;

To stain C. elegans with antibodies, the relatively impermeable cuticle must be bypassed by chemical or mechanical methods. "Freeze-cracking" is one method used to physically pull the cuticle from nematodes by compressing nematodes between two adherent slides, freezing them, and pulling the slides apart. Freeze-cracking provides a simple and rapid way to gain access to the tissues without chemical treatment and can be used with a variety of fixatives. However, it leads to the loss of many of the specimens and the required compression mechanically distorts the sample. Practice is required to maximize recovery of samples with good morphology. Freeze-cracking can be optimized for specific fixation conditions, recovery of samples, or low non-specific staining, but not for all parameters at once. For antibodies that require very hard fixation conditions and tolerate the chemical treatments needed to chemically permeabilize the cuticle, treatment of intact nematodes in solution may be preferred. If the antibody requires a lighter fix or if the optimum fixation conditions are unknown, freeze-cracking provides a very useful way to rapidly assay the antibody and can yield specific subcellular and cellular localization information for the antigen of interest.

When worms are properly compressed, cracked, and lightly fixed, virtually the entire worm can be accessible to antibody staining (see Figure 2). The location of the nuclei as indicated by DAPI staining indicates which parts of the worm are intact When the worms are subjected to a harder fixative, such as formaldehyde, the morphology of the worm may become distorted (as seen by the unnaturally wavy appearance of the muscles in Figures 3A-D). Another common problem is uneven fixation or pe...

Watch this Scientific Journal Video about Antibody Staining in C. Elegans Using "Freeze-Cracking" at JoVE.com

Antibody Staining in C. Elegans Using &quot;Freeze-Cracking&quot;

"Freeze-cracking," a method for exposing the inner tissues of the nematode C. elegans to antibodies for protein localization, is demonstrated.

Antibody Staining in C. Elegans Using &quot;Freeze-Cracking&quot;

To stain C.  elegans with antibodies, the relatively impermeable cuticle must be  bypassed by chemical or mechanical methods.  "Freeze-cracking" is one ...

antibody-staining-in-c-elegans-using-freeze-cracking

Research

JoVE Journal

Biology

Generation of Stable Transgenic C. elegans Using Microinjection

Transgenic Caenorhabditis elegans can be readily created via microinjection of a DNA plasmid solution into the gonad 1. The plasmid DNA rearranges to form extrachromosomal concatamers that are stably inherited, though not with the same efficiency as actual chromosomes 2. A gene of interest is co-injected with an obvious phenotypic marker, such as rol-6 or GFP, to allow selection of transgenic animals under a dissecting microscope. The exogenous gene may be expressed from its native promoter for cellular localization studies. Alternatively, the transgene can be driven by a different tissue-specific promoter to assess the role of the gene product in that particular cell or tissue. This technique efficiently drives gene expression in all tissues of C. elegans except for the germline or early embryo 3. Creation of transgenic animals is widely utilized for a range of experimental paradigms. This video demonstrates the microinjection procedure to generate transgenic worms. Furthermore, selection and maintenance of stable transgenic C. elegans lines is described.

This video demonstrates the technique of microinjection into the gonad of C. elegans to create transgenic animals.

Transgenic Caenorhabditis elegans can be readily created via microinjection of a DNA plasmid solution into the gonad 1.  The plasmid DNA rearranges to ...

Method for Whole Mount Antibody Staining in Chick

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying antibody expression in developing brain, neural tube and somite. This video demonstrates the different steps in whole-mount antibody staining using HRP conjugated secondary antibodies; First, the embryo is dissected from the egg and fixed in paraformaldehyde. Second, endogenous peroxidase is inactivated; The embryo is then exposed to primary antibody. After several washes, the embryo is incubated with secondary antibody conjugated to HRP. Peroxidase activity is revealed using reaction with diaminobenzidine substrate. Finally, the embryo is fixed and processed for photography and sectioning. The advantage of this method over the use of fluorescent antibodies is that embryos can be processed for wax sectioning, thus enabling the study of antigen sites in cross section. This method was originally introduced by Jane Dodd and Tom Jessell 1.

This video demonstrates whole mount immunohistochemistry, a method by which the spatial and temporal expression pattern of an antigen can be visualized in young chick embryos. This method was originally introduced by Jane Dodd and Tom Jessell.

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ...

Imaging C. elegans Embryos using an Epifluorescent Microscope and Open Source Software

Cellular processes, such as chromosome assembly, segregation and cytokinesis,are inherently dynamic. Time-lapse imaging of living cells, using fluorescent-labeled reporter proteins or differential interference contrast (DIC) microscopy, allows for the examination of the temporal progression of these dynamic events which is otherwise inferred from analysis of fixed samples1,2. Moreover, the study of the developmental regulations of cellular processes necessitates conducting time-lapse experiments on an intact organism during development. The Caenorhabiditis elegans embryo is light-transparent and has a rapid, invariant developmental program with a known cell lineage3, thus providing an ideal experiment model for studying questions in cell biology4,5and development6-9. C. elegans is amendable to genetic manipulation by forward genetics (based on random mutagenesis10,11) and reverse genetics to target specific genes (based on RNAi-mediated interference and targeted mutagenesis12-15). In addition, transgenic animals can be readily created to express fluorescently tagged proteins or reporters16,17. These traits combine to make it easy to identify the genetic pathways regulating fundamental cellular and developmental processes in vivo18-21. In this protocol we present methods for live imaging of C. elegans embryos using DIC optics or GFP fluorescence on a compound epifluorescent microscope. We demonstrate the ease with which readily available microscopes, typically used for fixed sample imaging, can also be applied for time-lapse analysis using open-source software to automate the imaging process.

Imaging C. elegans Embryos using an Epifluorescent Microscope and Open Source Software

The C. elegans embryo is a powerful system for studying cell biology and development. We present a protocol for live imaging of C. elegans embryos utilizing DIC optics or fluorescence using readily available epifluorescent microscopes and open-source software.

Cellular processes, such as chromosome assembly, segregation and cytokinesis,are inherently dynamic. Time-lapse imaging of living cells, using ...

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Synapses are composed of a presynaptic active zone in the signaling cell and a postsynaptic terminal in the target cell. In the case of chemical synapses, messages are carried by neurotransmitters released from presynaptic terminals and received by receptors on postsynaptic cells. Our previous research in Caenorhabditis elegans has shown that VSM-1 negatively regulates exocytosis. Additionally, analysis of synapses in vsm-1 mutants showed that animals lacking a fully functional VSM-1 have increased synaptic connectivity. Based on these preliminary findings, we hypothesized that C. elegans VSM-1 may play a crucial role in synaptogenesis. To test this hypothesis, double-labeled microarray analysis was performed, and gene expression profiles were determined. First, total RNA was isolated, reversely transcribed to cDNA, and hybridized to the DNA microarrays. Then, in-silico analysis of fluorescent probe hybridization revealed significant induction of many genes coding for members of the major sperm protein family (MSP) in mutants with enhanced synaptogenesis. MSPs are the major component of sperm in C. elegans and appear to signal nematode oocyte maturation and ovulation . In fruit flies, Chai and colleagues 1 demonstrated that MSP-like molecules regulate presynaptic bouton number and size at the neuromuscular junction. Moreover, analysis performed by Tsuda and coworkers 2 suggested that MSPs may act as ligands for Eph receptors and trigger receptor tyrosine kinase signaling cascades. Lastly, real time PCR analysis corroborated that the gene coding for MSP-32 is induced in vsm-1(ok1468) mutants. Taken together, research performed by our laboratory has shown that vsm-1 mutants have a significant increase in synaptic density, which could be mediated by MSP-32 signaling.

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Microarray analysis was conducted to determine genetic expression profiles in C. elegans, and real-time PCR was used to validate and quantify microarray data.

Synapses are composed of a presynaptic active zone in the signaling cell and a postsynaptic terminal in the target cell. In the case of chemical synapses, ...

RNAi Screening to Identify Postembryonic Phenotypes in C. elegans

C. elegans has proven to be a valuable model system for the discovery and functional characterization of many genes and gene pathways1. More sophisticated tools and resources for studies in this system are facilitating continued discovery of genes with more subtle phenotypes or roles. 
Here we present a generalized protocol we adapted for identifying C. elegans genes with postembryonic phenotypes of interest using RNAi2. This procedure is easily modified to assay the phenotype of choice, whether by light or fluorescence optics on a dissecting or compound microscope. This screening protocol capitalizes on the physical assets of the organism and molecular tools the C. elegans research community has produced. As an example, we demonstrate the use of an integrated transgene that expresses a fluorescent product in an RNAi screen to identify genes required for the normal localization of this product in late stage larvae and adults. First, we used a commercially available genomic RNAi library with full-length cDNA inserts. This library facilitates the rapid identification of multiple candidates by RNAi reduction of the candidate gene product. Second, we generated an integrated transgene that expresses our fluorecently tagged protein of interest in an RNAi-sensitive background. Third, by exposing hatched animals to RNAi, this screen permits identification of gene products that have a vital embryonic role that would otherwise mask a post-embryonic role in regulating the protein of interest. Lastly, this screen uses a compound microscope equipped for single cell resolution.

RNAi Screening to Identify Postembryonic Phenotypes in C. elegans

We describe a sensitized method to identify postembryonic regulators of protein expression and localization in C. elegans using an RNAi-based genomic screen and an integrated transgene that expresses a functional, fluorescently tagged protein.

C. elegans has proven to be a valuable model system for the discovery and functional characterization of many genes and gene pathways1. More sophisticated ...

C. elegans Chemotaxis Assay

Many organisms use chemotaxis to seek out food sources, avoid noxious substances, and find mates. Caenorhabditis elegans has impressive chemotaxis behavior.
 The premise behind testing the response of the worms to an odorant is to place them in an area and observe the movement evoked in response to an odorant. Even with the many available assays, optimizing worm starting location relative to both the control and test areas, while minimizing the interaction of worms with each other, while maintaining a significant sample size remains a work in progress 1-10. The method described here aims to address these issues by modifying the assay developed by Bargmann et al.1. A Petri dish is divided into four quadrants, two opposite quadrants marked "Test" and two are designated "Control". Anesthetic is placed in all test and control sites. The worms are placed in the center of the plate with a circle marked around the origin to ensure that non-motile worms will be ignored. Utilizing a four-quadrant system rather than one 2 or two 1 eliminates bias in the movement of the worms, as they are equidistant from test and control samples, regardless of which side of the origin they began. This circumvents the problem of worms being forced to travel through a cluster of other worms to respond to an odorant, which can delay worms or force them to take a more circuitous route, yielding an incorrect interpretation of their intended path. This method also shows practical advantages by having a larger sample size and allowing the researcher to run the assay unattended and score the worms once the allotted time has expired.

C. elegans Chemotaxis Assay

A method of quantitatively evaluating the chemotactic response of Caenorhabditis elegans is described. A chemotactic index (CI) was employed as a way to precisely evaluate the response of worms to certain targets, and serve as a platform of comparison between strains and compounds of interest.

Many organisms use chemotaxis to seek out food sources, avoid noxious substances, and find mates.  Caenorhabditis elegans has impressive chemotaxis ...

An Anoxia-starvation Model for Ischemia/Reperfusion in C. elegans

Protocols for anoxia/starvation in the genetic model organism C. elegans simulate ischemia/reperfusion. Worms are separated from bacterial food and placed under anoxia for 20 hr&#160;(simulated ischemia), and subsequently moved to a normal atmosphere with food (simulated reperfusion). This experimental paradigm results in increased death and neuronal damage, and techniques are presented to assess organism viability, alterations to the morphology of touch neuron processes, as well as touch sensitivity, which represents the behavioral output of neuronal function. Finally, a method for constructing hypoxic incubators using common kitchen storage containers is described. The addition of a mass flow control unit allows for alterations to be made to the gas mixture in the custom incubators, and a circulating water bath allows for both temperature control and makes it easy to identify leaks. This method provides a low cost alternative to commercially available units.

An Anoxia-starvation Model for Ischemia/Reperfusion in C. elegans

A protocol is described that uses anoxia/starvation in C. elegans to model ischemia/reperfusion. Functional outcomes include increased mortality, visible abnormalities in GFP-labeled neuronal processes, and impaired behavioral responses that require neuronal function.

Protocols for anoxia/starvation in the genetic model organism C. elegans simulate ischemia/reperfusion. Worms are separated from bacterial food and placed ...

Methods for Skin Wounding and Assays for Wound Responses in C. elegans

The C. elegans epidermis and cuticle form a simple yet sophisticated skin layer that can repair localized damage resulting from wounding. Studies of wound responses and repair in this model have illuminated our understanding of the cytoskeletal and genomic responses to tissue damage. The two most commonly used methods to wound the C. elegans adult skin are pricks with microinjection needles, and local laser irradiation. Needle wounding locally disrupts the cuticle, epidermis, and associated extracellular matrix, and may also damage internal tissues. Laser irradiation results in more localized damage. Wounding triggers a succession of readily assayed responses including elevated epidermal Ca2+ (seconds-minutes), formation and closure of an actin-containing ring at the wound site (1-2 hr), elevated transcription of antimicrobial peptide genes (2-24 hr), and scar formation. Essentially all wild type adult animals survive wounding, whereas mutants defective in wound repair or other responses show decreased survival. Detailed protocols for needle and laser wounding, and assays for quantitation and visualization of wound responses and repair processes (Ca dynamics, actin dynamics, antimicrobial peptide induction, and survival) are presented.

Methods for Skin Wounding and Assays for Wound Responses in C. elegans

The adult C. elegans skin is a tractable model for studies of epithelial wound responses, including wound closure, scar formation, and innate immunity.

The C. elegans epidermis and cuticle form a simple yet sophisticated skin layer that can repair localized damage resulting from wounding. Studies of wound ...

Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools

Quantitatively capturing developmental processes is crucial to derive mechanistic models and key to identify and describe mutant phenotypes. Here protocols are presented for preparing embryos and adult C. elegans animals for short- and long-term time-lapse microscopy and methods for tracking and quantification of developmental processes. The methods presented are all based on C. elegans strains available from the Caenorhabditis Genetics Center and on open-source software that can be easily implemented in any laboratory independently of the microscopy system used. A reconstruction of a 3D cell-shape model using the modelling software IMOD, manual tracking of fluorescently-labeled subcellular structures using the multi-purpose image analysis program Endrov, and an analysis of cortical contractile flow using PIVlab (Time-Resolved Digital Particle Image Velocimetry Tool for MATLAB) are shown. It is discussed how these methods can also be deployed to quantitatively capture other developmental processes in different models, e.g., cell tracking and lineage tracing, tracking of vesicle flow.

Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools

Here it is shown how to track and quantify developmental processes in C. elegans. The methods presented are based on open-source tools that can be easily implemented. It is demonstrated how to reconstruct 3D cell-shape models, how to manually track subcellular structures, and how to analyze cortical contractile flow.

Quantitatively capturing developmental processes is crucial to derive mechanistic models and key to identify and describe mutant phenotypes. Here ...

Measurements of Physiological Stress Responses in C. Elegans

Organisms are often exposed to fluctuating environments and changes in intracellular homeostasis, which can have detrimental effects on their proteome and physiology. Thus, organisms have evolved targeted and specific stress responses dedicated to repair damage and maintain homeostasis. These mechanisms include the unfolded protein response of the endoplasmic reticulum (UPRER), the unfolded protein response of the mitochondria (UPRMT), the heat shock response (HSR), and the oxidative stress response (OxSR). The protocols presented here describe methods to detect and characterize the activation of these pathways and their physiological consequences in the nematode, C. elegans. First, the use of pathway-specific fluorescent transcriptional reporters is described for rapid cellular characterization, drug screening, or large-scale genetic screening (e.g., RNAi or mutant libraries). In addition, complementary, robust physiological assays are described, which can be used to directly assess sensitivity of animals to specific stressors, serving as functional validation of the transcriptional reporters. Together, these methods allow for rapid characterization of the cellular and physiological effects of internal and external proteotoxic perturbations.

Measurements of Physiological Stress Responses in C. Elegans

Here, we characterize cellular proteotoxic stress responses in the nematode C. elegans by measuring the activation of fluorescent transcriptional reporters and assaying sensitivity to physiological stress.

Organisms are often exposed to fluctuating environments and changes in intracellular homeostasis, which can have detrimental effects on their proteome and ...