easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler

Nyaanga, Joy; Crombie, Timothy A.; Widmayer, Samuel J.; Andersen, Erik C.

doi:10.1371/journal.pone.0252000

Cited by 15 publications

(32 citation statements)

References 14 publications

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“…After 48 hours of growth, images of each well of animals were taken using an ImageXpress Nano (Molecular Devices, San Jose, CA). Images were analyzed using the easyXpress package (N yaanga et al . 2021), which facilitates the measurement of individual nematode sizes from images and calculates summary statistics for sizes of populations of nematodes.…”

Section: Methodsmentioning

confidence: 99%

Interactions of C. elegans β-tubulins with the microtubule inhibitor albendazole

Mains

Pallotto

Dilks³

et al. 2022

Preprint

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Parasitic nematodes are major human and agricultural pests, and benzimidazoles are amongst the most important broad spectrum anthelmintic drug class used for their control. Benzimidazole resistance is now widespread in many species of parasitic nematodes in livestock globally and an emerging concern for the sustainable control of human soil transmitted helminths. -tubulin is the major benzimidazole target, although other genes may influence resistance. Among the six C. elegans -tubulin genes, loss of ben-1 causes resistance without other apparent defects. Here, we explored the genetics of C. elegans -tubulin genes in relation to the response to the benzimidazole derivative albendazole. The most highly expressed -tubulin isotypes, encoded by tbb-1 and tbb-2, were known to be redundant with each other for viability, and their products are predicted not to bind benzimidazoles. We found that tbb-2 mutants, and to a lesser extent tbb-1 mutants, were hypersensitive to albendazole. The double mutant tbb-2 ben-1 is uncoordinated and dumpy, resembling the wild type exposed to albendazole, but the tbb-1 ben-1 double mutant did not show the same phenotype. These results suggest that tbb-2 is a modifier of ABZ sensitivity. To better understand how BEN-1 mutates to cause benzimidazole resistance, we isolated mutants resistant to albendazole and found that 15 of 16 mutations occurred in ben-1. Mutations ranged from likely nulls to hypomorphs, and several corresponded to residues that cause resistance in other organisms. Null alleles of ben-1 are albendazole-resistant and BEN-1 shows high sequence identity with tubulins from other organisms, suggesting that many amino acid changes could cause resistance. However, our results suggest that missense mutations conferring resistance are not evenly distributed across all possible conserved sites.

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Section: Methodsmentioning

confidence: 99%

Interactions of C. elegans β-tubulins with the microtubule inhibitor albendazole

Mains

Pallotto

Dilks³

et al. 2022

Preprint

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“…wrmXpress will work out-of-the-box for all datasets generated with an ImageXpress (Molecular Devices), which is a popular platform for worm labs [13,15,28,29]. For other endpoints, an HTD file must be provided, and the image data must be structured as in Fig 1.…”

Section: Conclusion and Future Developmentsmentioning

confidence: 99%

“…Regardless, in our hands the analysis of a full 96-well plate takes less than 3 hours using relatively modest hardware specifications (4 CPUs, 20 GB RAM). wrmXpress will work out-of-the-box for all datasets generated with an ImageXpress (Molecular Devices), which is a popular platform for worm labs [13,15,28,29]. For other endpoints, an HTD file must be provided, and the image data must be structured as in Fig 1 . However, the design of the pipelines is such that adding support for other platforms will be straightforward.…”

Section: Conclusion and Future Developmentsmentioning

confidence: 99%

“…Other developments in high-content imaging, sometimes combined with the employment of fluorescent stains to reveal fine-scale phenotypes, now allow for the quantification of detailed morphological and molecular features that can be used for image-based classification strategies [11][12][13][14]. Open-source packages have been developed to more readily handle large imaging datasets and provide quick readouts for quality control of entire experiments, plates, wells, and even individual worms [15]. Not unexpectedly, individual labs often develop their pipelines to suit their own needs.…”

Section: Introductionmentioning

confidence: 99%

“…These pipelines tend to focus on specific species and stages, require specific instrumentation, and demand an advanced grasp of compiled languages, resulting in siloed development and redundant rather than collaborative engineering efforts. There have been recent developments that unify parts of these efforts for the capture of phenotypes in model nematode species [15]. No package has yet to bring multiple phenotypes (i.e., motility and morphology) into a single framework that prioritizes flexibility across free-living and parasitic worms.…”

Section: Introductionmentioning

confidence: 99%

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wrmXpress: A modular package for high-throughput image analysis of parasitic and free-living worms

Wheeler

Garncarz

Gallo

et al. 2022

Preprint

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Advances in high-throughput and high-content imaging technologies require concomitant development of analytical software capable of handling large datasets and generating relevant phenotypic measurements. Several tools have been developed to analyze drug response phenotypes in parasitic and free-living worms, but these are siloed and often limited to specific instrumentation, worm species, and single phenotypes. No effort has been made to unify tools for analyzing high-content phenotypic imaging data of worms and provide a platform for future extensibility. We have developed wrmXpress, a unified framework for analyzing a variety of phenotypes matched to high-content experimental assays of free-living and parasitic nematodes and flatworms. We demonstrate its utility for analyzing a suite of phenotypes, including motility, development/size, and feeding, and establish the package as a platform upon which to build future custom phenotypic modules, including those that incorporate deep learning techniques. We show that wrmXpress can serve as an analytical workhorse for anthelmintic screening efforts across schistosomes, filarial nematodes, and free-living model nematodes, and holds promise for enabling collaboration among investigators with diverse interests.

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Orsay Virus Infection in Caenorhabditis elegans

Batachari,

Sarmiento,

Wernet

et al. 2024

Current Protocols

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Orsay virus infection in the nematode Caenorhabditis elegans presents an opportunity to study host‐virus interactions in an easily culturable, whole‐animal host. Previously, a major limitation of C. elegans as a model for studying antiviral immunity was the lack of viruses known to naturally infect the worm. With the 2011 discovery of the Orsay virus, a naturally occurring viral pathogen, C. elegans has emerged as a compelling model for research on antiviral defense. From the perspective of the host, the genetic tractability of C. elegans enables mechanistic studies of antiviral immunity while the transparency of this animal allows for the observation of subcellular processes in vivo. Preparing infective virus filtrate and performing infections can be achieved with relative ease in a laboratory setting. Moreover, several tools are available to measure the outcome of infection. Here, we describe workflows for generating infective virus filtrate, achieving reproducible infection of C. elegans, and assessing the outcome of viral infection using molecular biology approaches and immunofluorescence. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Preparation of Orsay virus filtrateSupport Protocol: Synchronize C. elegans development by bleachingBasic Protocol 2: Orsay virus infectionBasic Protocol 3: Quantification of Orsay virus RNA1/RNA2 transcript levels by qRT‐PCRBasic Protocol 4: Quantification of infection rate and fluorescence in situ hybridization (FISH) fluorescence intensityBasic Protocol 5: Immunofluorescent labeling of dsRNA in virus‐infected intestinal tissue

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easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler

Cited by 15 publications

References 14 publications

Interactions of C. elegans β-tubulins with the microtubule inhibitor albendazole

Interactions of C. elegans β-tubulins with the microtubule inhibitor albendazole

wrmXpress: A modular package for high-throughput image analysis of parasitic and free-living worms

Orsay Virus Infection in Caenorhabditis elegans

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