scholarly journals Mask R-CNN Based C. Elegans Detection with a DIY Microscope

Biosensors ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 257
Author(s):  
Sebastian Fudickar ◽  
Eike Jannik Nustede ◽  
Eike Dreyer ◽  
Julia Bornhorst
Keyword(s):  
Cell Biology ◽  
High Throughput Screening ◽  
Low Cost ◽  
Image Acquisition ◽  
Rapid Development ◽  
Model Organism ◽  
Large Data ◽  
Data Set ◽  
C Elegans ◽  
Do It Yourself

Caenorhabditis elegans (C. elegans) is an important model organism for studying molecular genetics, developmental biology, neuroscience, and cell biology. Advantages of the model organism include its rapid development and aging, easy cultivation, and genetic tractability. C. elegans has been proven to be a well-suited model to study toxicity with identified toxic compounds closely matching those observed in mammals. For phenotypic screening, especially the worm number and the locomotion are of central importance. Traditional methods such as human counting or analyzing high-resolution microscope images are time-consuming and rather low throughput. The article explores the feasibility of low-cost, low-resolution do-it-yourself microscopes for image acquisition and automated evaluation by deep learning methods to reduce cost and allow high-throughput screening strategies. An image acquisition system is proposed within these constraints and used to create a large data-set of whole Petri dishes containing C. elegans. By utilizing the object detection framework Mask R-CNN, the nematodes are located, classified, and their contours predicted. The system has a precision of 0.96 and a recall of 0.956, resulting in an F1-Score of 0.958. Considering only correctly located C. elegans with an [email protected] IoU, the system achieved an average precision of 0.902 and a corresponding F1 Score of 0.906.

scholarly journals Microfluidic Technologies for High Throughput Screening Through Sorting and On-Chip Culture of C. elegans

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4292 ◽  
Author(s):  
Daniel Midkiff ◽  
Adriana San-Miguel
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Model Organism ◽  
Large Data ◽  
Large Data Sets ◽  
Data Sets ◽  
C Elegans ◽  
Drug Candidates ◽  
On Chip ◽  
And Behavior

The nematode Caenorhabditis elegans is a powerful model organism that has been widely used to study molecular biology, cell development, neurobiology, and aging. Despite their use for the past several decades, the conventional techniques for growth, imaging, and behavioral analysis of C. elegans can be cumbersome, and acquiring large data sets in a high-throughput manner can be challenging. Developments in microfluidic “lab-on-a-chip” technologies have improved studies of C. elegans by increasing experimental control and throughput. Microfluidic features such as on-chip control layers, immobilization channels, and chamber arrays have been incorporated to develop increasingly complex platforms that make experimental techniques more powerful. Genetic and chemical screens are performed on C. elegans to determine gene function and phenotypic outcomes of perturbations, to test the effect that chemicals have on health and behavior, and to find drug candidates. In this review, we will discuss microfluidic technologies that have been used to increase the throughput of genetic and chemical screens in C. elegans. We will discuss screens for neurobiology, aging, development, behavior, and many other biological processes. We will also discuss robotic technologies that assist in microfluidic screens, as well as alternate platforms that perform functions similar to microfluidics.

scholarly journals A DIY Fabrication Approach for Ultra-Thin Focus-Tunable Liquid Lens Using Electrohydrodynamic Pump

Micromachines ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1452
Author(s):  
Taichi Murakami ◽  
Yu Kuwajima ◽  
Ardi Wiranata ◽  
Ayato Minaminosono ◽  
Hiroki Shigemune ◽  
...  
Keyword(s):  
Low Cost ◽  
Rapid Development ◽  
Pure Water ◽  
Dielectric Fluid ◽  
Copper Sheet ◽  
Fluidic Channel ◽  
Liquid Lens ◽  
Do It Yourself ◽  
Tunable Lenses ◽  
Smart Mobile

Demand for variable focus lens is increasing these days due to the rapid development of smart mobile devices and drones. However, conventional mechanical systems for lenses are generally complex, cumbersome, and rigid (e.g., for motors and gears). This research proposes a simple and compact liquid lens controlled by an electro hydro dynamics (EHD) pump. In our study, we propose a do-it-yourself (DIY) method to fabricate the low-cost EHD lens. The EHD lens consists of a polypropylene (PP) sheet for the exterior, a copper sheet for the electrodes, and an acrylic elastomer for the fluidic channel where dielectric fluid and pure water are filled. We controlled the lens magnification by changing the curvature of the liquid interface between the dielectric fluid and pure water. We evaluated the magnification performance of the lens. Moreover, we also established a numerical model to characterize the lens performance. We expect to contribute to the miniaturization of focus-tunable lenses.

scholarly journals Quantitative Analysis of Drug Efficacy on C. elegans Models for Neuromuscular Diseases

2021 ◽  
Author(s):  
Samuel Sofela ◽  
Sarah Sahloul ◽  
Yong-Ak Song
Keyword(s):  
Drug Screening ◽  
Low Cost ◽  
Neuromuscular Diseases ◽  
Model Organism ◽  
Drug Efficacy ◽  
Two Dimensional ◽  
C Elegans ◽  
Drug Candidates ◽  
High Throughput Drug Screening ◽  
Screening Assays

AbstractCaenorhabditis elegans has emerged as a powerful model organism for drug screening due to its cellular simplicity, genetic amenability and homology to humans combined with its small size and low cost. Currently, high-throughput drug screening assays are mostly based on image-based phenotyping not exploiting key locomotory parameters of this multicellular model with muscles such as its thrashing force, a critical parameter when screening drugs for muscle-related diseases. In this study, we demonstrated the use of a micropillar-based force assay chip in combination with an imaging assay to evaluate the efficacy of various drugs currently used in treatment of neuromuscular diseases. Using this two-dimensional approach, we showed that the force assay was generally more sensitive in measuring efficacy of drug treatment in Duchenne Muscular Dystrophy and Parkinson’s Disease mutant worms as well as partly in Amyotrophic Lateral Sclerosis model. These results underline the potential of our force assay chip in screening of potential drug candidates for the treatment of neuromuscular diseases when combined with an imaging assay in a two-dimensional analysis approach.

Multiple Roles of RNA Regulatory Factors in Neuronal Development and Function in C. elegans

2020 ◽  
Author(s):  
Matthew G. Andrusiak ◽  
Yishi Jin
Keyword(s):  
Nervous System ◽  
Cell Biology ◽  
Molecular Mechanisms ◽  
Neuronal Development ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Model Organism ◽  
Nervous System Development ◽  
Forward Genetics ◽  
C Elegans

Recent evidence has highlighted the dynamic nature of mRNA regulation, particularly in the nervous system, from complex pre-mRNA processing to long-range transport and long-term storage of mature mRNAs. In accordance with the importance for mRNA-mediated regulation of nervous system development and maintenance, various mutations in RNA-binding proteins are associated with a range of human disorders. C. elegans express many RNA-binding factors that have human orthologs and perform similar biochemical functions. This chapter focuses on the research using C. elegans to dissect molecular mechanisms involving mRNA-mediated pathways. It highlights the key approaches and findings that integrate genetic and genomic studies in the nervous system. The analyses of genetic mutants, primarily using forward genetics, offer functional insights for genes important for neuronal development, synaptic transmission, and neuronal repair. In combination with single-neuron cell biology and cell-type genomics, the knowledge learned from this model organism has continued to lead to ground-breaking discoveries.

scholarly journals Artificial Neural Network—Based Analysis of High-Throughput Screening Data for Improved Prediction of Active Compounds

2009 ◽  
Vol 14 (10) ◽  
pp. 1236-1244 ◽  
Author(s):  
Swapan Chakrabarti ◽  
Stan R. Svojanovsky ◽  
Romana Slavik ◽  
Gunda I. Georg ◽  
George S. Wilson ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Back Propagation ◽  
Large Data ◽  
Classification Performance ◽  
Data Sets ◽  
Data Set ◽  
Active Compounds ◽  
Physicochemical Features ◽  
Artificial Neural

Artificial neural networks (ANNs) are trained using high-throughput screening (HTS) data to recover active compounds from a large data set. Improved classification performance was obtained on combining predictions made by multiple ANNs. The HTS data, acquired from a methionine aminopeptidases inhibition study, consisted of a library of 43,347 compounds, and the ratio of active to nonactive compounds, R A/N, was 0.0321. Back-propagation ANNs were trained and validated using principal components derived from the physicochemical features of the compounds. On selecting the training parameters carefully, an ANN recovers one-third of all active compounds from the validation set with a 3-fold gain in R A/N value. Further gains in RA/N values were obtained upon combining the predictions made by a number of ANNs. The generalization property of the back-propagation ANNs was used to train those ANNs with the same training samples, after being initialized with different sets of random weights. As a result, only 10% of all available compounds were needed for training and validation, and the rest of the data set was screened with more than a 10-fold gain of the original RA/N value. Thus, ANNs trained with limited HTS data might become useful in recovering active compounds from large data sets.

scholarly journals Biophysical analysis of drug efficacy on C. elegans models for neurodegenerative and neuromuscular diseases

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0246496
Author(s):  
Samuel Sofela ◽  
Sarah Sahloul ◽  
Yong-Ak Song
Keyword(s):  
Drug Screening ◽  
Low Cost ◽  
Neuromuscular Diseases ◽  
Model Organism ◽  
Drug Efficacy ◽  
Fluorescence Assay ◽  
Two Dimensional ◽  
Biophysical Parameter ◽  
C Elegans ◽  
Drug Candidates

Caenorhabditis elegans has emerged as a powerful model organism for drug screening due to its cellular simplicity, genetic amenability and homology to humans combined with its small size and low cost. Currently, high-throughput drug screening assays are mostly based on image-based phenotyping with the focus on morphological-descriptive traits not exploiting key locomotory parameters of this multicellular model with muscles such as its thrashing force, a critical biophysical parameter when screening drugs for muscle-related diseases. In this study, we demonstrated the use of a micropillar-based force assay chip in combination with a fluorescence assay to evaluate the efficacy of various drugs currently used in treatment of neurodegenerative and neuromuscular diseases. Using this two-dimensional approach, we showed that the force assay was generally more sensitive in measuring efficacy of drug treatment in Duchenne Muscular Dystrophy and Parkinson’s Disease mutant worms as well as partly in Amyotrophic Lateral Sclerosis model. These results underline the potential of our force assay chip in screening of potential drug candidates for the treatment of neurodegenerative and neuromuscular diseases when combined with a fluorescence assay in a two-dimensional analysis approach.

scholarly journals Old knowledge and new technologies allow rapid development of model organisms

2016 ◽  
Vol 27 (6) ◽  
pp. 882-887 ◽  
Author(s):  
Charles E. Cook ◽  
Janet Chenevert ◽  
Tomas A. Larsson ◽  
Detlev Arendt ◽  
Evelyn Houliston ◽  
...  
Keyword(s):  
Cell Biology ◽  
High Throughput Sequencing ◽  
Biological Diversity ◽  
New Technologies ◽  
Low Cost ◽  
Rapid Development ◽  
Experimental Models ◽  
Model Organisms ◽  
Model Species ◽  
Cellular Mechanisms

Until recently the set of “model” species used commonly for cell biology was limited to a small number of well-understood organisms, and developing a new model was prohibitively expensive or time-consuming. With the current rapid advances in technology, in particular low-cost high-throughput sequencing, it is now possible to develop molecular resources fairly rapidly. Wider sampling of biological diversity can only accelerate progress in addressing cellular mechanisms and shed light on how they are adapted to varied physiological contexts. Here we illustrate how historical knowledge and new technologies can reveal the potential of nonconventional organisms, and we suggest guidelines for selecting new experimental models. We also present examples of nonstandard marine metazoan model species that have made important contributions to our understanding of biological processes.

The Use of Inquiry-Based Activities with Caenorhabditis elegans to Enable Students to Learn about UV Radiation

2017 ◽  
Vol 79 (5) ◽  
pp. 401-406
Author(s):  
Fran Norflus
Keyword(s):  
Caenorhabditis Elegans ◽  
Uv Radiation ◽  
Cell Biology ◽  
Genetic Background ◽  
Model Organism ◽  
Microbiology Laboratory ◽  
C Elegans ◽  
Laboratory Activities ◽  
Introductory Class ◽  
Different Strains

In traditional microbiology laboratory activities, different strains of bacteria are exposed to UV radiation for varying lengths of time. This article provides information that expands on these activities (or uses them alone) with Caenorhabditis elegans as a model organism with which to study the effects of UV radiation. These activities might be used in an introductory class to teach students the basics of working with C. elegans. In cell biology and microbiology classes, students might learn about how UV radiation can damage cells and cause cancer. These activities can also be used to teach the students about how genetic background can affect the sensitivity to UV radiation. In the laboratory, the students design their own activities by altering the parameters of the basic UV radiation experiment. By performing these laboratory activities, students will learn about UV radiation and about all parts of the scientific process.

Zebrafish: gaining popularity in lipid research

2010 ◽  
Vol 429 (2) ◽  
pp. 235-242 ◽  
Author(s):  
Maarit Hölttä-Vuori ◽  
Veijo T. V. Salo ◽  
Lena Nyberg ◽  
Christian Brackmann ◽  
Annika Enejder ◽  
...  
Keyword(s):  
Genetic Manipulation ◽  
Imaging Techniques ◽  
Low Cost ◽  
Rapid Development ◽  
Model Organism ◽  
Lipoprotein Metabolism ◽  
Lipid Absorption ◽  
Whole Body ◽  
Lipid Research ◽  
Biological Phenomena

Zebrafish are an increasingly popular vertebrate model organism in which to study biological phenomena. It has been widely used, especially in developmental biology and neurobiology, and many aspects of its development and physiology are similar to those of mammals. The popularity of zebrafish relies on its relatively low cost, rapid development and ease of genetic manipulation. Moreover, the optical transparency of the developing fish together with novel imaging techniques enable the direct visualization of complex phenomena at the level of the entire organism. This potential is now also being increasingly appreciated by the lipid research community. In the present review we summarize basic information on the lipid composition and distribution in zebrafish tissues, including lipoprotein metabolism, intestinal lipid absorption, the yolk lipids and their mobilization, as well as lipids in the nervous system. We also discuss studies in which zebrafish have been employed for the visualization of whole-body lipid distribution and trafficking. Finally, recent advances in using zebrafish as a model for lipid-related diseases, including atherosclerosis, obesity, diabetes and hepatic steatosis are highlighted. As the insights into zebrafish lipid metabolism increase, it is likely that zebrafish as a model organism will become an increasingly powerful tool in lipid research.

scholarly journals Germline Stem and Progenitor Cell Aging in C. elegans

2021 ◽  
Vol 9 ◽  
Author(s):  
Theadora Tolkin ◽  
E. Jane Albert Hubbard
Keyword(s):  
Stem Cells ◽  
Cell Biology ◽  
Progenitor Cell ◽  
Model Organism ◽  
Cell Aging ◽  
Germline Stem Cells ◽  
C Elegans ◽  
Age Related ◽  
Stem And Progenitor Cells ◽  
Molecular Aspects

Like many animals and humans, reproduction in the nematode C. elegans declines with age. This decline is the cumulative result of age-related changes in several steps of germline function, many of which are highly accessible for experimental investigation in this short-lived model organism. Here we review recent work showing that a very early and major contributing step to reproductive decline is the depletion of the germline stem and progenitor cell pool. Since many cellular and molecular aspects of stem cell biology and aging are conserved across animals, understanding mechanisms of age-related decline of germline stem and progenitor cells in C. elegans has broad implications for aging stem cells, germline stem cells, and reproductive aging.

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