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438 results for “Caenorhabditis elegans”
Detecting Changes in the Caenorhabditis elegans Intestinal Environment Using an Engineered Bacterial Biosensor
<p>Data for the figures in the manuscript <br> <a href="https://pubs.acs.org/doi/10.1021/acssynbio.9b00166">https://pubs.acs.org/doi/10.1021/acssynbio.9b00166</a></p> <p>Abstract:<br> <em>Caenorhabditis elegans</em> has become a key model organism within biology. In particular, the transparent gut, rapid growing time, and ability to create a defined gut microbiota make it an ideal candidate organism for understanding and engineering the host microbiota. Here we present the development of an experimental model that can be used to characterize whole-cell bacterial biosensors <em>in vivo</em>. A dual-plasmid sensor system responding to isopropyl β-d-1-thiogalactopyranoside was developed and fully characterized <em>in vitro</em>. Subsequently, we show that the sensor was capable of detecting and reporting on changes in the intestinal environment of <em>C. elegans</em> after introducing an exogenous inducer into the environment. The protocols presented here may be used to aid the rational design of engineered bacterial circuits, primarily for diagnostic applications. In addition, the model system may serve to reduce the use of current animal models and aid in the exploration of complex questions within general nematode and host–microbe biology.</p>
Phase response analyses support a relaxation oscillator model of locomotor rhythm generation in Caenorhabditis elegans
<p>This dataset contains all data and codes that are used in the manuscript entitled "Phase response analyses support a relaxation oscillator model of locomotor rhythm generation in <em>Caenorhabditis elegans</em>".</p> <p>The data include raw videos and intermediate data for optogenetic experiments of all strains, experimental conditions (illumination duration, illuminated region, fluid viscosity and date). Within the parent folder 'Videos', each subfolder represents data of a group of experiments using the same strain under the same condition, as indicated explicitly by the subfolder name. Within each subfolder, there are raw videos of freely moving worms perturbed by transient optogenetic perturbations and intermediate data which include locomotory information and the corresponding figure plots (kymographs) that were generated by analysing the raw videos with the image analysis software (also in the dataset)</p> <p>The codes include scripts for image data analysis and model simulations. The image data analysis codes include scripts specifically for generating phase portrait graphs, phase response curves, head oscillation stability plots, phase isochron map and vector field. The model simulation codes include scripts for model oscillators implementation, paramter estimation/optimization and simulations of optogenetic inhibition.</p>
Using single-worm data to quantify heterogeneity in Caenorhabditis elegans-bacterial interactions
<p>The nematode <em>Caenorhabditis elegans</em> is a model system for host-microbe and host-microbiome interactions. Many studies to date use batch digests rather than individual worm samples to quantify bacterial load in this organism. Here it is argued that the large inter-individual variability seen in bacterial colonization of the <em>C. elegans</em> intestine is informative, and that batch digest methods discard information that is important for accurate comparison across conditions. As describing the variation inherent to these samples requires large numbers of individuals, a convenient 96-well plate protocol for disruption and colony plating of individual worms is established.</p>
Figure 3 in Chemotaxis of Caenorhabditis elegans Toward Volatile Organic Compounds from Stropharia rugosoannulata Induced by Amino Acids
Figure 3: Chemotaxis (percent attracted) and mortality (percent of attracted worms dead) in the groups supplemented with L-phenylalanine or L-tryptophan and the control without amino acids. The error bars indicate standard deviation. The statistical differences were analyzed using one-way ANOVA, *P <0.05, **P <0.01.
Figure 2 in Chemotaxis of Caenorhabditis elegans Toward Volatile Organic Compounds from Stropharia rugosoannulata Induced by Amino Acids
Figure 2: GC-MS total ion chromatography of different samples. A: L-phenylalanine alone, strain 1.202 alone and strain cultured on water agar plus L-phenylalanine, benzaldehyde was increased and 1-Octen-3-ol was newly produced from strain 1.2052 cultures added L-phenylalanine; B: strain 1.202 alone, L-tyrosine alone and strain cultured on water agar plus L-tyrosine, benzaldehyde was decreased and 1-Octen-3-ol and indole were newly produced were produced from strain 1.2052 cultures added L-tyrosine.
Figure 1 in Chemotaxis of Caenorhabditis elegans Toward Volatile Organic Compounds from Stropharia rugosoannulata Induced by Amino Acids
Figure 1: Chemotaxis (percent attracted) of Caenorhabditis elegans toward Stropharia rugosoannulata stain 1.2052 cultured on water agar supplemented with amino acids. Controls are phenylalanine or tyrosine alone and strain 1.2052 alone. The error bars indicate standard deviation. The statistical differences were analyzed using one-way ANOVA, *P<0.05, **P<0.01.
Figure S2 in Reproductive Span of Caenorhabditis elegans Is Extended by Microbacterium sp.
Figure S2: Protorhabditis sp. CFB231 make sperm. (A) DIC image of spermathecal region (outlined). One oocyte is apparently transiting the spermatheca. (B) DAPI staining for nuclei. (C) Merged images of DIC and DAPI. DIC, differential interference contrast.
Figure S1 in Reproductive Span of Caenorhabditis elegans Is Extended by Microbacterium sp.
Figure S1: Size comparison of the four tested nematode species grown on Microbacterium sp. CFBb37 and Escherichia coli OP50. Images are representative samples.
Figure 3 in Reproductive Span of Caenorhabditis elegans Is Extended by Microbacterium sp.
Figure 3: Summary of RS extension in the Caenorhabditis species (orange) and the outgroup Protorhabditis sp. (light blue). Red lines indicate inferred ancestral evolutionary lineages with extended RS. We suggest that other species within the genus Caenorhabditis are likely to have extended RS but this is untested. For simplification, some species are not listed and are grouped together in triangles, with the numbers of known species indicated. Phylogeny is adapted from Kiontke and Fitch (2005) and Felix et al. (2014) with the position of Protorhabditis sp. CFB231 placed next to P. sp. 1 species based on the 18S ribosomal RNA gene sequence (Zhang et al., 2000; Morgulis et al., 2008). Protorhabditis sp. CFB231 is self-fertile but the sexual system, hermaphroditic or parthenogenetic, is unknown (indicated by a question mark). RS, reproductive span.
Figure 2 in Reproductive Span of Caenorhabditis elegans Is Extended by Microbacterium sp.
Figure 2: Lifespan assays of C. elegans on Microbacterium sp. CFBb37 and the OP50 control. C. elegans grown on CFBb37 survived longer than OP50 (P <0.001, log-rank test). Detailed lifespan data are in Tables S4 and S5.
Figure 1 in Reproductive Span of Caenorhabditis elegans Is Extended by Microbacterium sp.
Figure 1: RS of individual nematodes on Microbacterium sp. CFBb37 and the E. coli OP50 control. (A) C. elegans, (B) C. briggsae, (C) C. tropicalis, and (D) Protorhabditis sp. on CFBb37 had longer RS than on OP50 (P <0.001, log-rank test). Full RS data in Table 2. RS, reproductive span.
Data accompanying "HSP70 inhibits CHIP E3 ligase activity to maintain germline function in Caenorhabditis elegans" article.
<p>This work was funded by the National Science Centre, Poland (grant PRELUDIUM number 2021/41/N/NZ1/03086) (to P.T.) and by the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation) under Germany’s Excellence Strategy – EXC 2030 – 390661388 and – FOR 5504 – project number 496650118 (to T.H.). M.T.P. received support by the Cologne Graduate School of Aging Research. N.A.S., A.S., K.J., and M.N. were supported by the International Institute of Molecular and Cell Biology in Warsaw.</p>
Diet can alter the cost of resistance to a natural parasite in Caenorhabditis elegans
<p>Resistance to parasites confers a fitness advantage, yet hosts show substantial variation in resistance in natural populations. Evolutionary theory indicates that resistant and susceptible genotypes can coexist if resistance is costly, but there is mixed evidence that resistant individuals have lower fitness in the absence of parasites. One explanation for this discrepancy is that the cost of resistance varies with environmental context. We tested this hypothesis using Caenorhabditis elegans and its natural microsporidian parasite, Nematocida ironsii. We used multiple metrics to compare the fitness of two near-isogenic host genotypes differing at regions associated with resistance to N. ironsii. To quantify the effect of the environment on the cost associated with these known resistance regions, we measured fitness on three microbial diets. We found that the cost of resistance varied with both diet and the measure of fitness. We detected no cost to resistance, irrespective of diet, when fitness was measured as fecundity. However, we detected a cost when fitness was measured in terms of population growth, and the magnitude of this cost varied with diet. These results provide a proof-of-concept that, by mediating the cost of resistance, environmental context may govern the rate and nature of resistance evolution in heterogeneous environments.</p>
Diet can alter the cost of resistance to a natural parasite in Caenorhabditis elegans
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Using single-worm data to quantify heterogeneity in Caenorhabditis elegans-bacterial interactions
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Phase response analyses support a relaxation oscillator model of locomotor rhythm generation in Caenorhabditis elegans
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Short-term heritable variation overwhelms two hundred generations of mutational variance for metabolic traits in Caenorhabditis elegans
<p>Metabolic disorders have a large heritable component, and have increased markedly in human populations over the past few generations. Genome-wide association studies of metabolic traits typically find a substantial unexplained fraction of total heritability, suggesting an important role of spontaneous mutation. An alternative explanation is that epigenetic effects contribute significantly to the heritable variation. Here we report a study designed to quantify the cumulative effects of spontaneous mutation on adenosine metabolism in the nematode <i>Caenorhabditis elegans</i>, including both the activity and concentration of two metabolic enzymes and the standing pools of their associated metabolites. The only prior studies on the effects of mutation on metabolic enzyme activity, in <i>Drosophila melanogaster</i>, found that total enzyme activity presents a mutational target similar to that of morphological and life-history traits. However, those studies were not designed to account for short-term heritable effects. We find that the short-term heritable variance for most traits is of similar magnitude as the variance among MA lines. This result suggests that the potential heritable effects of epigenetic variation in metabolic disease warrant additional scrutiny.</p>
Phenotypic stasis despite genetic divergence and differentiation in Caenorhabditis elegans.
<p># Data for the manuscript : Phenotypic stasis despite genetic divergence and differentiation in Caenorhabditis elegans.</p><p>https://doi.org/10.1101/2022.05.28.493856</p><p> </p><p>The data directory contains:</p><p>- the raw transition rates in Final_merged_data_NGM.txt</p><p>- population male frequencies estimates : population_rep_male_freqs.txt</p><p>- fertility data from the Cemee: fertility.rda (from Noble et al. 2017)</p><p>- Mean state frequencies in the movies : State_freq_NGM.txt</p><p> </p><p>The Rcode directory contains all code to reproduce the analysis is available on github:</p><p>https://github.com/ExpEvolWormLab/Mallard_Stasis</p>
Hypoxia-inducible factor induces cysteine dioxygenase and promotes cysteine homeostasis in Caenorhabditis elegans
<p>Dedicated genetic pathways regulate cysteine homeostasis. For example, high levels of cysteine activate cysteine dioxygenase, a key enzyme in cysteine catabolism in most animal and many fungal species. The mechanism by which cysteine dioxygenase is regulated is largely unknown. In an unbiased genetic screen for mutations that activate cysteine dioxygenase (<em>cdo-1</em>) in the nematode <em>C. elegans, </em>we isolated loss-of-function mutations in <em>rhy-1 </em>and <em>egl-9, </em>which encode proteins that negatively regulate the stability or activity of the oxygen-sensing hypoxia-inducible transcription factor (<em>hif-1</em>). EGL-9 and HIF-1 are core members of the conserved eukaryotic hypoxia response. However, we demonstrate that the mechanism of HIF-1-mediated induction of <em>cdo-1 </em>is largely independent of EGL-9 prolyl hydroxylase activity and the von Hippel-Lindau E3 ubiquitin ligase, the classical hypoxia signaling pathway components. We demonstrate that <em>C. elegans cdo-1 </em>is transcriptionally activated by high levels of cysteine and <em>hif-1</em>. <em>hif-1-</em>dependent activation of <em>cdo-1</em> occurs downstream of an H<sub>2</sub>S-sensing pathway that includes <em>rhy-1, cysl-1, </em>and <em>egl-9.</em> <em>cdo-1 </em>transcription is primarily activated in the hypodermis where it is also sufficient to drive sulfur amino acid metabolism. Thus, the regulation of <em>cdo-1 </em>by <em>hif-1 </em>reveals a negative feedback loop that maintains cysteine homeostasis. High levels of cysteine stimulate the production of an H<sub>2</sub>S signal. H<sub>2</sub>S then acts through the <em>rhy-1/cysl-1/egl-9 </em>signaling pathway to increase HIF-1-mediated transcription of <em>cdo-1, </em>promoting the degradation of cysteine via CDO-1.</p>
Automated Dual Olfactory Device for Studying Head/Tail Chemosensation in Caenorhabditis elegans
<p>A microfluidic device for simultaneous delivery of olfactory stimuli to the head and the tail of immobilized C elegans to visualize Calcium activity in the nervous system.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.