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Measuring Oxygen Consumption Rate in Caenorhabditis elegans

Featured protocol,  Authors: Konstantinos Palikaras
Konstantinos PalikarasAffiliation: Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Crete, Greece
Bio-protocol author page: a3832
 and Nektarios Tavernarakis
Nektarios TavernarakisAffiliation: Department of Basic Sciences, Faculty of Medicine, University of Crete, Crete, Greece
For correspondence: tavernarakis@imbb.forth.gr
Bio-protocol author page: a3833
date: 12/5/2016, 44 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.2049.

Brief version appeared in Nature, May 2015
The rate of oxygen consumption is a vital marker indicating cellular function during lifetime under normal or metabolically challenged conditions. It is used broadly to study mitochondrial function (Artal-Sanz and Tavernarakis, 2009; Palikaras et al., 2015; Ryu et al., 2016) or investigate factors mediating the switch from oxidative phosphorylation to aerobic glycolysis (Chen et al., 2015; Vander Heiden et al., 2009). In this protocol, we describe a method for the determination of oxygen consumption rates in the nematode Caenorhabditis elegans.

Intracellular Assessment of ATP Levels in Caenorhabditis elegans

Featured protocol,  Authors: Konstantinos Palikaras
Konstantinos PalikarasAffiliation: Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Crete, Greece
Bio-protocol author page: a3832
 and Nektarios Tavernarakis
Nektarios TavernarakisAffiliation 1: Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Crete, Greece
Affiliation 2: Department of Basic Sciences, Faculty of Medicine, University of Crete, Crete, Greece
For correspondence: tavernarakis@imbb.forth.gr
Bio-protocol author page: a3833
date: 12/5/2016, 29 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.2048.

Brief version appeared in Nature, May 2015
Eukaryotic cells heavily depend on adenosine triphosphate (ATP) generated by oxidative phosphorylation (OXPHOS) within mitochondria. ATP is the major energy currency molecule, which fuels cell to carry out numerous processes, including growth, differentiation, transportation and cell death among others (Khakh and Burnstock, 2009). Therefore, ATP levels can serve as a metabolic gauge for cellular homeostasis and survival (Artal-Sanz and Tavernarakis, 2009; Gomes et al., 2011; Palikaras et al., 2015). In this protocol, we describe a method for the determination of intracellular ATP levels using a bioluminescence approach in the nematode Caenorhabditis elegans.

Measuring Oxygen Consumption Rate in Caenorhabditis elegans

Authors: Konstantinos Palikaras
Konstantinos PalikarasAffiliation: Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Crete, Greece
Bio-protocol author page: a3832
 and Nektarios Tavernarakis
Nektarios TavernarakisAffiliation: Department of Basic Sciences, Faculty of Medicine, University of Crete, Crete, Greece
For correspondence: tavernarakis@imbb.forth.gr
Bio-protocol author page: a3833
date: 12/5/2016, 44 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.2049.

[Abstract] The rate of oxygen consumption is a vital marker indicating cellular function during lifetime under normal or metabolically challenged conditions. It is used broadly to study mitochondrial function (Artal-Sanz and Tavernarakis, 2009; Palikaras et al., 2015; Ryu et al., 2016) or investigate factors mediating ...

Intracellular Assessment of ATP Levels in Caenorhabditis elegans

Authors: Konstantinos Palikaras
Konstantinos PalikarasAffiliation: Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Crete, Greece
Bio-protocol author page: a3832
 and Nektarios Tavernarakis
Nektarios TavernarakisAffiliation 1: Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Crete, Greece
Affiliation 2: Department of Basic Sciences, Faculty of Medicine, University of Crete, Crete, Greece
For correspondence: tavernarakis@imbb.forth.gr
Bio-protocol author page: a3833
date: 12/5/2016, 29 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.2048.

[Abstract] Eukaryotic cells heavily depend on adenosine triphosphate (ATP) generated by oxidative phosphorylation (OXPHOS) within mitochondria. ATP is the major energy currency molecule, which fuels cell to carry out numerous processes, including growth, differentiation, transportation and cell death among others ...

Artificial Optogenetic TRN Stimulation of C. elegans

Authors: Ithai Rabinowitch
Ithai RabinowitchAffiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, USA
For correspondence: ithairab@gmail.com
Bio-protocol author page: a3605
Millet Treinin
Millet TreininAffiliation: Department of Medical Neurobiology, Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
Bio-protocol author page: a3606
 and Jihong Bai
Jihong BaiAffiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, USA
Bio-protocol author page: a3607
date: 10/20/2016, 148 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1966.

[Abstract] Optogenetics is a powerful tool for manipulating neuronal activity with high temporal and spatial precision. In the nematode C. elegans optogentics is especially useful and easy to apply. This is because C. elegans is translucent, so its neurons are highly accessible to optic stimulation. In addition, ...

Evaluation of Burkholderia cepacia Complex Bacteria Pathogenicity Using Caenorhabditis elegans

Authors: Pietro Tedesco
Pietro TedescoAffiliation: Institute of Protein Biochemistry, National Research Council, Naples, Italy
Bio-protocol author page: a3599
Elia Di Schiavi
Elia Di SchiaviAffiliation: Institute of Bioscience and Bioresources, National Research Council, Naples, Italy
Bio-protocol author page: a3600
Fortunato Palma Esposito
Fortunato Palma EspositoAffiliation: Institute of Protein Biochemistry, National Research Council, Naples, Italy
Bio-protocol author page: a3601
 and Donatella de Pascale
Donatella de PascaleAffiliation: Institute of Protein Biochemistry, National Research Council, Naples, Italy
For correspondence: d.depascale@ibp.cnr.it
Bio-protocol author page: a3602
date: 10/20/2016, 156 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1964.

[Abstract] This protocol describes two biological assays to evaluate pathogenicity of Burkholderia cepacia complex (Bcc) strains against the nematode Caenorhabditis elegans. Specifically, these two assays allow one to identify if the under-investigated Bcc strains are able to kill the nematodes by intestinal colonization ...

Root-knot Nematode Penetration and Sclareol Nematicidal Activity Assays

Authors: Taketo Fujimoto
Taketo FujimotoAffiliation 1: National Agriculture and Food Research Organization Hokkaido Agricultural Research Center, Sapporo, Japan
Affiliation 2: National Agricultural Research Center, Tsukuba, Japan
For correspondence: taketof@affrc.go.jp
Bio-protocol author page: a3247
Takayuki Mizukubo
Takayuki MizukuboAffiliation: National Agricultural Research Center, Tsukuba, Japan
Bio-protocol author page: a3248
Hiroshi Abe
Hiroshi AbeAffiliation: Department of Biological Systems, RIKEN BioResource Center, Tsukuba, Japan
Bio-protocol author page: a3249
 and Shigemi Seo
Shigemi SeoAffiliation 1: National Agricultural Research Center, Tsukuba, Japan
Affiliation 2: National Institute of Agrobiological Science, Tsukuba, Japan
For correspondence: sseo71@affrc.go.jp
Bio-protocol author page: a3250
date: 6/20/2016, 616 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1848.

[Abstract] Plant parasitic nematodes parasitize roots and/or stems of various plants thereby inhibiting absorption of nutrients and moisture. In particular, root-knot nematodes (RKN) are group of the most devastating pests. Various techniques, such as soil sterilization, cultivation of resistant crops, and chemical ...

Isolation of Nippostrongylus brasiliensis Larvae from Mouse Lungs

Authors: Mali Camberis
Mali CamberisAffiliation: Malaghan Institute of Medical Research, Wellington, New Zealand
Bio-protocol author page: a2917
Tiffany Bouchery
Tiffany BoucheryAffiliation: École Polytechnique Fédérale De Lausanne, Lausanne, Switzerland
Bio-protocol author page: a2918
 and Graham Le Gros
Graham Le GrosAffiliation: Malaghan Institute of Medical Research, Wellington, New Zealand
For correspondence: glegros@malaghan.org.nz
Bio-protocol author page: a2919
date: 2/20/2016, 1048 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1736.

[Abstract] The rodent parasite Nippostrongylus brasiliensis (N. brasiliensis) models the salient features of helminth infection including skin penetration, migration from tissues to lung, maturation and egg production in the gut. As a potent activator of systemic and mucosal Th2 immune responses, Nippostrongylus ...

Dye Labeling of Live Nippostrongylus brasiliensis Larvae for Visualization in Host Tissue

Authors: Tiffany Bouchery
Tiffany BoucheryAffiliation: École Polytechnique Fédérale De Lausanne, Lausanne, Switzerland
Bio-protocol author page: a2918
Mali Camberis
Mali CamberisAffiliation: Malaghan Institute of Medical Research, Wellington, New Zealand
Bio-protocol author page: a2917
 and Graham Le Gros
Graham Le GrosAffiliation: Malaghan Institute of Medical Research, Wellington, New Zealand
For correspondence: glegros@malaghan.org.nz
Bio-protocol author page: a2919
date: 2/20/2016, 747 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1737.

[Abstract] Visualization of the interaction between parasitic nematodes and their host enables a better understanding of the development of the nematode during the infectious stages of its life cycle and of the effects of host response on nematode integrity in tissues. Appropriate live imaging of these nematode/host ...

Infection Assay of Cyst Nematodes on Arabidopsis Roots

Authors: Holger Bohlmann
Holger BohlmannAffiliation: Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
For correspondence: holger.bohlmann@boku.ac.at
Bio-protocol author page: a2561
 and Krzysztof Wieczorek
Krzysztof WieczorekAffiliation: Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
For correspondence: krzysztof.wieczorek@boku.ac.at
Bio-protocol author page: a2562
date: 9/20/2015, 1335 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1596.

[Abstract] Plant parasitic nematodes are devastating pests on many crops. Juveniles (J2) of cyst nematodes invade the roots to induce a syncytium. This feeding site is their only source of nutrients. Male nematodes leave the roots after the fourth molt to mate with females. The females stay attached to their syncytia ...

Chemotaxis and Jumping Assays in Nematodes

Authors: Tiffany Baiocchi
Tiffany BaiocchiAffiliation: Department of Nematology, University of California, Riverside, USA
Bio-protocol author page: a2536
 and Adler R. Dillman
Adler R. DillmanAffiliation: Department of Nematology, University of California, Riverside, USA
For correspondence: adler.dillman@ucr.edu
Bio-protocol author page: a2537
date: 9/20/2015, 1102 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1587.

[Abstract] Nematodes have sensitive olfactory perception, which is used to detect and differentiate many volatile odorants. Some odorants are attractive, others repulsive, and yet others evoke no particular response. Chemotaxis assays can be used to determine the role of certain odors in many different behaviors ...

Labeling of the Intestinal Lumen of Caenorhabditis elegans by Texas Red-dextran Feeding

Authors: Keiko Saegusa
Keiko SaegusaAffiliation: Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
Bio-protocol author page: a2479
 and Ken Sato
Ken SatoAffiliation: Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
For correspondence: sato-ken@gunma-u.ac.jp
Bio-protocol author page: a2480
date: 8/20/2015, 1110 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1564.

[Abstract] In this method, the intestinal lumen of Caenorhabditis elegans (C. elegans) is labeled with a fluorescent fluid-phase marker, Texas Red-dextran. Since dextran conjugates are membrane impermeable, animals fed with it show a red fluorescent signal in the lumen of the intestine. Texas Red-dextran in the ...
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[Bio101] Common Worm Media and Buffers

Author: Fanglian He date: 4/5/2011, 20654 views, 9 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.55.

[Abstract] Here are recipes of some media and solutions often used in C. elegans research....

[Bio101] Lifespan Assay

Author: Fanglian He date: 4/5/2011, 13162 views, 3 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.57.

[Abstract] This assay is used to address aging-related questions in worms....

[Bio101] Total RNA Extraction from C. elegans

Author: Fanglian He date: 3/20/2011, 12923 views, 1 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.47.

[Abstract] This protocol describes total RNA extraction from worms with or without using commercial RNA extraction kits....

[Bio101] Making Males of C. elegans

Author: Fanglian He date: 4/20/2011, 12249 views, 2 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.58.

[Abstract] Getting males from a hermaphrodite population. This is a modified version of protocol originally written by Michael Koelle at Yale University....

[Bio101] RNA Interference (RNAi) by Bacterial Feeding

Author: Fanglian He date: 4/20/2011, 12006 views, 1 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.59.

[Abstract] There are 3 ways to perform RNAi in worms: microinjection, soaking and feeding. In the feeding protocol, RNAi is induced by cultivating worms on bacteria expressing gene-specific dsRNA. dsRNA is expressed in E. coli and ingested by worms. This protocol describes the feeding protocol to induce RNAi....

[Bio101] Synchronization of Worm

Author: Fanglian He date: 4/5/2011, 11794 views, 1 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.56.

[Abstract] Attaining a large synchronized population of worms is desirable for use in some assays in order to eliminate variation in results due to age differences. Two ways to get synchronized worms include egg preparation via bleaching and egg lay. The former in general yields more progeny than the latter, however, ...

PCR-RFLP Genotyping of Point Mutations in Caenorhabditis elegans

Author: Peichuan Zhang
Peichuan ZhangAffiliation: Department of Biochemistry and Biophysics, University of California, San Francisco, USA
For correspondence: peichuan.zhang@ucsf.edu
Bio-protocol author page: a11
date: 3/20/2012, 11244 views, 3 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.128.

[Abstract] This protocol describes the basic principle of PCR/restriction digest genotyping of point mutations in worms, based on the principle of Restriction Fragment Length Polymorphism (RFLP) analysis. This type of genotyping is, particularly, useful when phenotypic analysis of animals carrying point mutations ...

[Bio101] Oil Red O Staining of Fixed Worm

Author: Fanglian He date: 7/5/2012, 10870 views, 1 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.230.

[Abstract] Oil red O staining is used to assess major fat stores in C. elegans. This protocol is adapted from the Ashrafi Lab at the University of California-San Francisco....

[Bio101] DAPI Nuclear Staining of Live Worm

Author: Fanglian He date: 6/5/2011, 9470 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.77.

[Abstract] Adapted from the Villenueve Lab at Stanford University. This is a very simple method using ethanol fixation, but works very well....

[Bio101] Single Worm PCR

Author: Fanglian He date: 4/20/2011, 8737 views, 1 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.60.

[Abstract] This protocol is used for genotyping single worms....
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