scholarly journals Paper-Supported High-Throughput 3D Culturing, Trapping, and Monitoring of Caenorhabditis Elegans

Micromachines ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 99 ◽  
Author(s):  
Mehdi Tahernia ◽  
Maedeh Mohammadifar ◽  
Seokheun Choi
Keyword(s):  
High Throughput ◽  
Developmental Stages ◽  
3D Culture ◽  
Natural Habitats ◽  
Paper Substrate ◽  
C Elegans ◽  
Cultivation Technique ◽  
Plastic Frame ◽  
Pass Through ◽  
High Throughput Imaging

We developed an innovative paper-based platform for high-throughput culturing, trapping, and monitoring of C. elegans. A 96-well array was readily fabricated by placing a nutrient-replenished paper substrate on a micromachined 96-well plastic frame, providing high-throughput 3D culturing environments and in situ analysis of the worms. The paper allows C. elegans to pass through the porous and aquatic paper matrix until the worms grow and reach the next developmental stages with the increased body size comparable to the paper pores. When the diameter of C. elegans becomes larger than the pore size of the paper substrate, the worms are trapped and immobilized for further high-throughput imaging and analysis. This work will offer a simple yet powerful technique for high-throughput sorting and monitoring of C. elegans at a different larval stage by controlling and choosing different pore sizes of paper. Furthermore, we developed another type of 3D culturing system by using paper-like transparent polycarbonate substrates for higher resolution imaging. The device used the multi-laminate structure of the polycarbonate layers as a scaffold to mimic the worm’s 3D natural habitats. Since the substrate is thin, mechanically strong, and largely porous, the layered structure allowed C. elegans to move and behave freely in 3D and promoted the efficient growth of both C. elegans and their primary food, E. coli. The transparency of the structure facilitated visualization of the worms under a microscope. Development, fertility, and dynamic behavior of C. elegans in the 3D culture platform outperformed those of the standard 2D cultivation technique.

DevStaR: High-Throughput Quantification of C. elegans Developmental Stages

2013 ◽  
Vol 32 (10) ◽  
pp. 1791-1803 ◽  
Author(s):  
Amelia G. White ◽  
Brandon Lees ◽  
Huey-Ling Kao ◽  
P. Giselle Cipriani ◽  
Eliana Munarriz ◽  
...  
Keyword(s):  
High Throughput ◽  
Developmental Stages ◽  
C Elegans

scholarly journals A high-throughput imaging and nuclear segmentation analysis protocol for cleared 3D culture models

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Molly E. Boutin ◽  
Ty C. Voss ◽  
Steven A. Titus ◽  
Kennie Cruz-Gutierrez ◽  
Sam Michael ◽  
...  
Keyword(s):  
High Throughput ◽  
3D Culture ◽  
Segmentation Analysis ◽  
Culture Models ◽  
High Throughput Imaging ◽  
Nuclear Segmentation ◽  
Analysis Protocol

scholarly journals Behavioral fingerprints predict insecticide and anthelmintic mode of action

2021 ◽  
Author(s):  
Adam McDermott-Rouse ◽  
Eleni Minga ◽  
Ida Barlow ◽  
Luigi Feriani ◽  
Philippa H Harlow ◽  
...  
Keyword(s):  
High Throughput ◽  
Mode Of Action ◽  
Behavioral Responses ◽  
Physiological Data ◽  
Discovery Process ◽  
Crucial Step ◽  
C Elegans ◽  
Modes Of Action ◽  
Automated Phenotyping ◽  
High Throughput Imaging

AbstractNovel invertebrate-killing compounds are required in agriculture and medicine to overcome resistance to existing treatments. Because insecticides and anthelmintics are discovered in phenotypic screens, a crucial step in the discovery process is determining the mode of action of hits. Visible whole-organism symptoms are combined with molecular and physiological data to determine mode of action. However, manual symptomology is laborious and requires symptoms that are strong enough to see by eye. Here we use high-throughput imaging and quantitative phenotyping to measure C. elegans behavioral responses to compounds and train a classifier that predicts mode of action with an accuracy of 88% for a set of ten common modes of action. We also classify compounds within each mode of action to discover pharmacological relationships that are not captured in broad mode of action labels. High-throughput imaging and automated phenotyping could therefore accelerate mode of action discovery in invertebrate-targeting compound development and help to refine mode of action categories.

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

2021 ◽  
Author(s):  
Joy Nyaanga ◽  
Timothy A. Crombie ◽  
Samuel J. Widmayer ◽  
Erik C Andersen
Keyword(s):  
High Throughput ◽  
Imaging Techniques ◽  
R Package ◽  
Summary Statistics ◽  
Data Filtering ◽  
Analysis Pipeline ◽  
C Elegans ◽  
Visualization Of Data ◽  
Microscopy Data ◽  
High Throughput Imaging

High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput microscopy data in the R environment. The package provides a logical workflow for the reading, analysis, and visualization of data generated using CellProfiler’s WormToolbox. We equipped easyXpress with powerful functions to customize the filtering of noise in data, specifically by identifying and removing objects that deviate from expected animal measurements. This flexibility in data filtering allows users to optimize their analysis pipeline to match their needs. In addition, easyXpress includes tools for generating detailed visualizations, allowing the user to interactively compare summary statistics across wells and plates with ease. Researchers studying C. elegans benefit from this streamlined and extensible package as it is complementary to CellProfiler and leverages the R environment to rapidly process and analyze large high-throughput imaging datasets.

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

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0252000
Author(s):  
Joy Nyaanga ◽  
Timothy A. Crombie ◽  
Samuel J. Widmayer ◽  
Erik C. Andersen
Keyword(s):  
High Throughput ◽  
Imaging Techniques ◽  
R Package ◽  
Summary Statistics ◽  
Data Filtering ◽  
Analysis Pipeline ◽  
C Elegans ◽  
Visualization Of Data ◽  
Microscopy Data ◽  
High Throughput Imaging

High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput microscopy data in the R environment. The package provides a logical workflow for the reading, analysis, and visualization of data generated using CellProfiler’s WormToolbox. We equipped easyXpress with powerful functions to customize the filtering of noise in data, specifically by identifying and removing objects that deviate from expected animal measurements. This flexibility in data filtering allows users to optimize their analysis pipeline to match their needs. In addition, easyXpress includes tools for generating detailed visualizations, allowing the user to interactively compare summary statistics across wells and plates with ease. Researchers studying C. elegans benefit from this streamlined and extensible package as it is complementary to CellProfiler and leverages the R environment to rapidly process and analyze large high-throughput imaging datasets.

scholarly journals A microfluidic platform for lifelong high-resolution and high throughput imaging of subtle aging phenotypes in C. elegans

Lab on a Chip ◽  
2018 ◽  
Vol 18 (20) ◽  
pp. 3090-3100 ◽  
Author(s):  
Sahand Saberi-Bosari ◽  
Javier Huayta ◽  
Adriana San-Miguel
Keyword(s):  
High Resolution ◽  
High Throughput ◽  
Structure And Function ◽  
Neuronal Structure ◽  
Microfluidic Platform ◽  
C Elegans ◽  
And Function ◽  
High Throughput Imaging

Aging produces a number of changes in the neuronal structure and function throughout a variety of organisms.

A Semi-high-throughput Imaging Method and Data Visualization Toolkit to Analyze C. elegans Embryonic Development

10.3791/60362 ◽  
2019 ◽  
Author(s):  
Renat N. Khaliullin ◽  
Jeffrey M. Hendel ◽  
Adina Gerson-Gurwitz ◽  
Shaohe Wang ◽  
Stacy D. Ochoa ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Data Visualization ◽  
High Throughput ◽  
Imaging Method ◽  
C Elegans ◽  
Visualization Toolkit ◽  
High Throughput Imaging

scholarly journals A high-throughput device for size based separation of C. elegans developmental stages

Lab on a Chip ◽  
2014 ◽  
Vol 14 (10) ◽  
pp. 1746-1752 ◽  
Author(s):  
Xiaoni Ai ◽  
Weipeng Zhuo ◽  
Qionglin Liang ◽  
Patrick T. McGrath ◽  
Hang Lu
Keyword(s):  
Caenorhabditis Elegans ◽  
High Throughput ◽  
Developmental Stages ◽  
C Elegans ◽  
Size Based Separation

We present an efficient and fast device for size-based separation of Caenorhabditis elegans.

scholarly journals QsRNA-seq: a method for high-throughput profiling and quantifying small RNAs

2018 ◽  
Author(s):  
Alla Fishman ◽  
Dean Light ◽  
Ayelet T. Lamm
Keyword(s):  
High Throughput ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Biological Research ◽  
C Elegans ◽  
Cellular Processes ◽  
Repetitive Nature ◽  
Developmental Role ◽  
Non Coding Rnas

The finding that small non-coding RNAs (sRNAs) can affect cellular processes by regulating gene expression had a significant impact on biological research and clinical diagnosis. Yet, the ability to quantify and profile sRNAs, specifically miRNAs, using high-throughput sequencing is especially challenging because of their small size and repetitive nature. We developed QsRNA-seq, a method for preparation of sRNA libraries for high-throughput sequencing that overcomes this difficulty by enabling separation of fragments shorter than 100nt long that differ only by 20nt in length. The method supports using unique molecular identifiers for quantification. We show that QsRNA-seq gives very accurate, comprehensive and reproducible results. Using QsRNA-seq to study the miRNA repertoire in C. elegans embryo and L4 larval developmental stages, enabled extending the list of miRNAs that are expressed in a developmental-specific manner. Interestingly, we found that miRNAs 23nt long are predominantly expressed in developmental stage L4, suggesting a possible connection between the length of miRNA and its developmental role.

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