Intestinal Ca2+ wave dynamics in freely moving C. elegans coordinate execution of a rhythmic motor program

Defecation in the nematode worm Caenorhabditis elegans is a highly rhythmic behavior that is regulated by a Ca2+ wave generated in the 20 epithelial cells of the intestine, in part through activation of the inositol 1,4,5-trisphosphate receptor. Execution of the defecation motor program (DMP) can be modified by external cues such as nutrient availability or mechanical stimulation. To address the likelihood that environmental regulation of the DMP requires integrating distinct cellular and organismal processes, we have developed a method for studying coordinate Ca2+ oscillations and defecation behavior in intact, freely behaving animals. We tested this technique by examining how mutations in genes known to alter Ca2+ handling [including egl-8/phospholipase C (PLC)-β, kqt-3/KCNQ1, sca-1/sarco(endo)plasmic reticulum Ca2+ ATPase, and unc-43/Ca2+-CaMKII] contribute to shaping the Ca2+ wave and asked how Ca2+ wave dynamics in the mutant backgrounds altered execution of the DMP. Notably, we find that Ca2+ waves in the absence of PLCβ initiate ectopically, often traveling in reverse, and fail to trigger a complete DMP. These results suggest that the normal supremacy of the posterior intestinal cells is not obligatory for Ca2+ wave occurrence but instead helps to coordinate the DMP. Furthermore, we present evidence suggesting that an underlying pacemaker appears to oscillate at a faster frequency than the defecation cycle and that arrhythmia may result from uncoupling the pacemaker from the DMP rather than from disrupting the pacemaker itself. We also show that chronic elevations in Ca2+ have limited influence on the defecation period but instead alter the interval between successive steps of the DMP. Finally, our results demonstrate that it is possible to assess Ca2+ dynamics and muscular contractions in a completely unrestrained model organism.

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Model super-organisms: Can the biochemical genetics of E. coli help us understand aging?

The Biochemist ◽

10.1042/bio03704012 ◽

2015 ◽

Vol 37 (4) ◽

pp. 12-15

Author(s):

David Weinkove

Keyword(s):

Biosynthetic Pathway ◽

Model Organism ◽

Toxin Production ◽

Enzyme Function ◽

Nutrient Media ◽

E Coli ◽

C Elegans ◽

Biochemical Pathways ◽

Nematode Worm ◽

Worm Caenorhabditis Elegans

Escherichia coli is a powerful model organism to help us understand biochemical pathways and enzyme function. In E. coli, biosynthetic pathway mutants are conditionally viable depending on the composition of the nutrient media. Genetic analysis allows enzyme function to be linked to gene sequences. E. coli is used in the lab as a food source for the nematode worm Caenorhabditis elegans, a model organism for the understanding of basic animal biology. Recent work has shown that specific biosynthetic pathways in E. coli can influence C. elegans aging. Careful experimentation is needed to determine whether E. coli biochemistry influences aging by altering C. elegans nutrition or through changes to bacterial functions, such as toxin production. Understanding these interactions in the C. elegans–E. coli model “super-organism” will inform studies of how bacteria of the human microbiota interact with the host.

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Recurrent Neural Networks with Interpretable Cells Predict and Classify Worm Behaviour

10.1101/222208 ◽

2017 ◽

Cited By ~ 6

Author(s):

Kezhi Li ◽

Avelino Javer ◽

Eric E. Keaveny ◽

Andre E.X. Brown

Keyword(s):

Generative Models ◽

Sensor Technology ◽

Test Analysis ◽

Artificial Neuron ◽

C Elegans ◽

Large Databases ◽

Artificial Neurons ◽

Mutant Strains ◽

Freely Behaving ◽

Nematode Worm

AbstractAn important goal in behaviour analytics is to connect disease state or genome variation with observable differences in behaviour. Despite advances in sensor technology and imaging, informative behaviour quantification remains challenging. The nematode worm C. elegans provides a unique opportunity to test analysis approaches because of its small size, compact nervous system, and the availability of large databases of videos of freely behaving animals with known genetic differences. Despite its relative simplicity, there are still no reports of generative models that can capture essential differences between even well-described mutant strains. Here we show that a multilayer recurrent neural network (RNN) can produce diverse behaviours that are difficult to distinguish from real worms’ behaviour and that some of the artificial neurons in the RNN are interpretable and correlate with observable features such as body curvature, speed, and reversals. Although the RNN is not trained to perform classification, we find that artificial neuron responses provide features that perform well in worm strain classification.

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Soil nematode Caenorhabditis elegans Maupas as a convenient model organism to study anthelmintic activity of plant extracts

E3S Web of Conferences ◽

10.1051/e3sconf/202017602002 ◽

2020 ◽

Vol 176 ◽

pp. 02002

Author(s):

Anastasia Egorova ◽

Rufina Kolsanova ◽

Albina Nigmatullina ◽

Rifgat Shagidullin ◽

Tatiana Kalinnikova

Keyword(s):

Model Organism ◽

Anthelmintic Activity ◽

Motor Program ◽

Raw Material ◽

Toxic Action ◽

Soil Nematode ◽

Active Components ◽

C Elegans ◽

Nicotinic Cholinoreceptors ◽

Dose Dependent

The article deals with the study of the possibility to use free-living soil nematode C. elegans in researches of anthelmintic activity of plant raw material. A. sativum juice and aqueous extract of T. vulgare flowers were used in experiments. It is shown that both A. sativum juice and tansy flowers extract caused dose-dependent disturbances of C. elegans swimming motor program. These disturbances are similar with disturbances caused by agonist of cholinoreceptors levamisole. Therefore, the target of A. sativum juice and T. vulgare extract action is C. elegans cholinergic system. The mechanism of toxic action of A. sativum and T. vulgare on C. elegans organism consists in hyperactivation of nicotinic cholinoreceptors. The possibility of quick adaptation of C. elegans nicotinic cholinoreceptors to active components of tansy flowers extract was revealed. Soil nematode C. elegans may be used for investigation of anthelmintic activity of A. sativum and T. vulgare for the purpose of identification of secondary metabolites responsible for the toxic action on helminths.

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5. Uncontrolled Cell Division and Migration of Q neuroblasts in mutant strains of C. elegans

Inquiry@Queen's Undergraduate Research Conference Proceedings ◽

10.24908/iqurcp.10065 ◽

2018 ◽

Author(s):

Brandon Lam

Keyword(s):

Cell Division ◽

Cell Metabolism ◽

Model Organism ◽

C Elegans ◽

Mutant Strains ◽

Increase Risk ◽

And Migration ◽

Nematode Worm

Cancer is one of the most prevalent and deadly diseases in today's society, affecting millions of people around the globe. Uncontrolled cell division and migration which are two of the six major hallmarks of cancer have been studied extensively in vitro, however in vivo these hallmarks are not well understood. We used the Caenorhabditis elegans nematode worm as our model organism in order to study these two hallmarks. In unfavorable environmental conditions such as starvation, C. elegans can enter a developmental arrest in where certain cell metabolism ceases to continue, this stage is known as L1 arrest. Normally in L1 arrested worms, there are 2 distinct Q neuroblast cells which are precursors of sensory and interneurons that do not divide and migrate. However, when we mutate certain genes, we noticed that the two Q neuroblasts inappropriately divided and migrated, this suggests that we have identified a good model to study uncontrolled cell division and migration. We have already found one gene that when mutated, results in the Q neuroblasts inappropriately dividing and migrating at L1 arrest, now we are looking for other mutated genes that can cause this phenotype, this ultimately allows us to identify new mechanisms that cause an increase risk in cancer.

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The glycomes of Caenorhabditis elegans and other model organisms

Biochemical Society Symposium ◽

10.1042/bss0690117 ◽

2002 ◽

Vol 69 ◽

pp. 117-134 ◽

Cited By ~ 47

Author(s):

Stuart M. Haslam ◽

David Gems ◽

Howard R. Morris ◽

Anne Dell

Keyword(s):

Caenorhabditis Elegans ◽

Current Knowledge ◽

Structural Data ◽

Model Organisms ◽

Entire Genome ◽

C Elegans ◽

The Face ◽

Area Of Concern ◽

Nematode Worm

There is no doubt that the immense amount of information that is being generated by the initial sequencing and secondary interrogation of various genomes will change the face of glycobiological research. However, a major area of concern is that detailed structural knowledge of the ultimate products of genes that are identified as being involved in glycoconjugate biosynthesis is still limited. This is illustrated clearly by the nematode worm Caenorhabditis elegans, which was the first multicellular organism to have its entire genome sequenced. To date, only limited structural data on the glycosylated molecules of this organism have been reported. Our laboratory is addressing this problem by performing detailed MS structural characterization of the N-linked glycans of C. elegans; high-mannose structures dominate, with only minor amounts of complex-type structures. Novel, highly fucosylated truncated structures are also present which are difucosylated on the proximal N-acetylglucosamine of the chitobiose core as well as containing unusual Fucα1–2Gal1–2Man as peripheral structures. The implications of these results in terms of the identification of ligands for genomically predicted lectins and potential glycosyltransferases are discussed in this chapter. Current knowledge on the glycomes of other model organisms such as Dictyostelium discoideum, Saccharomyces cerevisiae and Drosophila melanogaster is also discussed briefly.

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Health and longevity studies in C. elegans: the “healthy worm database” reveals strengths, weaknesses and gaps of test compound-based studies

Biogerontology ◽

10.1007/s10522-021-09913-2 ◽

2021 ◽

Vol 22 (2) ◽

pp. 215-236

Author(s):

Nadine Saul ◽

Steffen Möller ◽

Francesca Cirulli ◽

Alessandra Berry ◽

Walter Luyten ◽

...

Keyword(s):

Healthy Aging ◽

Model Organism ◽

Research Field ◽

Aging Research ◽

Genetic Manipulations ◽

C Elegans ◽

Starting Point ◽

Health Related ◽

Phenotype Measurement ◽

Or Gene

AbstractSeveral biogerontology databases exist that focus on genetic or gene expression data linked to health as well as survival, subsequent to compound treatments or genetic manipulations in animal models. However, none of these has yet collected experimental results of compound-related health changes. Since quality of life is often regarded as more valuable than length of life, we aim to fill this gap with the “Healthy Worm Database” (http://healthy-worm-database.eu). Literature describing health-related compound studies in the aging model Caenorhabditis elegans was screened, and data for 440 compounds collected. The database considers 189 publications describing 89 different phenotypes measured in 2995 different conditions. Besides enabling a targeted search for promising compounds for further investigations, this database also offers insights into the research field of studies on healthy aging based on a frequently used model organism. Some weaknesses of C. elegans-based aging studies, like underrepresented phenotypes, especially concerning cognitive functions, as well as the convenience-based use of young worms as the starting point for compound treatment or phenotype measurement are discussed. In conclusion, the database provides an anchor for the search for compounds affecting health, with a link to public databases, and it further highlights some potential shortcomings in current aging research.

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Benefits of Using the Invertebrate Model Organism C. Elegans in an Inquiry-Based Laboratory Activity

Teaching of Psychology ◽

10.1177/00986283211029649 ◽

2021 ◽

pp. 009862832110296

Author(s):

Angy J. Kallarackal

Keyword(s):

American Psychological Association ◽

Model Organism ◽

Learning Goals ◽

Research Skills ◽

Final Exam ◽

Laboratory Activity ◽

Writing Ability ◽

C Elegans ◽

Invertebrate Model ◽

Laboratory Experiences

Background: The goals of laboratory experiences include developing knowledge base, research skills, and scientific communication abilities. Objective: The aim was to assess an inquiry-based laboratory activity using the model organism Caenorhabditis elegans in relation to learning goals. Method: Students in a Biopsychology laboratory course worked in groups to test the effect of various drugs (e.g., nicotine, ethanol, fluoxetine, and melatonin) on C. elegans behavior. The activity included literature review, experimental design, and a final lab report. A cumulative final exam included a synaptic communication question related to the content of the activity. Results: Students showed better retention of laboratory-related content compared to other topics from the course, as demonstrated through performance on the final exam and were able to replicate previous research demonstrating effects of drug on locomotion. However, students did not improve writing ability compared to performance on a previous American Psychological Association style lab report. Conclusion: This study demonstrates that using a student-designed, multi-week laboratory assignment in an undergraduate Biopsychology course supports the growth of psychology knowledge and the development of research skills. Teaching Implications: Instructors should consider using the described laboratory activity for biopsychology or behavioral neuroscience classes or consider similarly designed laboratory formats for other courses in Psychology.

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Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature

Database ◽

10.1093/database/baab015 ◽

2021 ◽

Vol 2021 ◽

Author(s):

Valerio Arnaboldi ◽

Jaehyoung Cho ◽

Paul W Sternberg

Keyword(s):

Search Engines ◽

Complex Structure ◽

Model Organism ◽

Gene Interaction ◽

Relevant Information ◽

Biomedical Literature ◽

C Elegans ◽

Word Clouds ◽

Scientific Papers ◽

Model Organism Databases

Abstract Finding relevant information from newly published scientific papers is becoming increasingly difficult due to the pace at which articles are published every year as well as the increasing amount of information per paper. Biocuration and model organism databases provide a map for researchers to navigate through the complex structure of the biomedical literature by distilling knowledge into curated and standardized information. In addition, scientific search engines such as PubMed and text-mining tools such as Textpresso allow researchers to easily search for specific biological aspects from newly published papers, facilitating knowledge transfer. However, digesting the information returned by these systems—often a large number of documents—still requires considerable effort. In this paper, we present Wormicloud, a new tool that summarizes scientific articles in a graphical way through word clouds. This tool is aimed at facilitating the discovery of new experimental results not yet curated by model organism databases and is designed for both researchers and biocurators. Wormicloud is customized for the Caenorhabditis elegans literature and provides several advantages over existing solutions, including being able to perform full-text searches through Textpresso, which provides more accurate results than other existing literature search engines. Wormicloud is integrated through direct links from gene interaction pages in WormBase. Additionally, it allows analysis on the gene sets obtained from literature searches with other WormBase tools such as SimpleMine and Gene Set Enrichment. Database URL: https://wormicloud.textpressolab.com

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Behavioral Effects of Volatile Anesthetics in Caenorhabditis elegans

Anesthesiology ◽

10.1097/00000542-199610000-00027 ◽

1996 ◽

Vol 85 (4) ◽

pp. 901-912 ◽

Cited By ~ 38

Author(s):

Michael C. Crowder ◽

Laynie D. Shebester ◽

Tim Schedl

Keyword(s):

Nervous System ◽

Caenorhabditis Elegans ◽

Time Course ◽

Model Organism ◽

Volatile Anesthetic ◽

Volatile Anesthetics ◽

Effective Concentration ◽

Forward Genetics ◽

C Elegans ◽

Median Effective Concentration

Background The nematode Caenorhabditis elegans offers many advantages as a model organism for studying volatile anesthetic actions. It has a simple, well-understood nervous system; it allows the researcher to do forward genetics; and its genome will soon be completely sequenced. C. elegans is immobilized by volatile anesthetics only at high concentrations and with an unusually slow time course. Here other behavioral dysfunctions are considered as anesthetic endpoints in C. elegans. Methods The potency of halothane for disrupting eight different behaviors was determined by logistic regression of concentration and response data. Other volatile anesthetics were also tested for some behaviors. Established protocols were used for behavioral endpoints that, except for pharyngeal pumping, were set as complete disruption of the behavior. Time courses were measured for rapid behaviors. Recovery from exposure to 1 or 4 vol% halothane was determined for mating, chemotaxis, and gross movement. All experiments were performed at 20 to 22 degrees C. Results The median effective concentration values for halothane inhibition of mating (0.30 vol%-0.21 mM), chemotaxis (0.34 vol%-0.24 mM), and coordinated movement (0.32 vol% - 0.23 mM) were similar to the human minimum alveolar concentration (MAC; 0.21 mM). In contrast, halothane produced immobility with a median effective concentration of 3.65 vol% (2.6 mM). Other behaviors had intermediate sensitivities. Halothane's effects reached steady-state in 10 min for all behaviors tested except immobility, which required 2 h. Recovery was complete after exposure to 1 vol% halothane but was significantly reduced after exposure to immobilizing concentrations. Conclusions Volatile anesthetics selectively disrupt C. elegans behavior. The potency, time course, and recovery characteristics of halothane's effects on three behaviors are similar to its anesthetic properties in vertebrates. The affected nervous system molecules may express structural motifs similar to those on vertebrate anesthetic targets.

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