Microfluidic approaches for Caenorhabditis elegans research

C. elegans foraging as a model for understanding the neuronal basis of decision-making

Animals have evolved to seek, select, and exploit food sources in their environment. Collectively termed foraging, these ubiquitous behaviors are necessary for animal survival. As a foundation for understanding foraging, behavioral ecologists established early theoretical and mathematical frameworks which have been subsequently refined and supported by field and laboratory studies of foraging animals. These simple models sought to explain how animals decide which strategies to employ when locating food, what food items to consume, and when to explore the environment for new food sources. These foraging decisions involve integration of prior experience with multimodal sensory information about the animal's current environment and internal state. We suggest that the nematode Caenorhabditis elegans is well-suited for a high-resolution analysis of complex goal-oriented behaviors such as foraging. We focus our discussion on behavioral studies highlighting C. elegans foraging on bacteria and summarize what is known about the underlying neuronal and molecular pathways. Broadly, we suggest that this simple model system can provide a mechanistic understanding of decision-making and present additional avenues for advancing our understanding of complex behavioral processes.

Caenorhabditis elegans as an in vivo model for the identification of natural antioxidants with anti-aging actions

Natural antioxidants have recently emerged as a highly exciting and significant topic in anti-aging research. Diverse organism models present a viable protocol for future research. Notably, many breakthroughs on natural antioxidants have been achieved in the nematode Caenorhabditis elegans, an animal model frequently utilized for the study of aging research and anti-aging drugs in vivo. Due to the conservation of signaling pathways on oxidative stress resistance, lifespan regulation, and aging disease between C. elegans and multiple high-level organisms (humans), as well as the low and controllable cost of time and labor, it gradually develops into a trustworthy in vivo model for high-throughput screening and validation of natural antioxidants with anti-aging actions. First, information and models on free radicals and aging are presented in this review. We also describe indexes, detection methods, and molecular mechanisms for studying the in vivo antioxidant and anti-aging effects of natural antioxidants using C. elegans. It includes lifespan, physiological aging processes, oxidative stress levels, antioxidant enzyme activation, and anti-aging pathways. Furthermore, oxidative stress and healthspan improvement induced by natural antioxidants in humans and C. elegans are compared, to understand the potential and limitations of the screening model in preclinical studies. Finally, we emphasize that C. elegans is a useful model for exploring more natural antioxidant resources and uncovering the mechanisms underlying aging-related risk factors and diseases.

Deep Learning for Microfluidic-Assisted Caenorhabditis elegans Multi-Parameter Identification Using YOLOv7

The Caenorhabditis elegans (C. elegans) is an ideal model organism for studying human diseases and genetics due to its transparency and suitability for optical imaging. However, manually sorting a large population of C. elegans for experiments is tedious and inefficient. The microfluidic-assisted C. elegans sorting chip is considered a promising platform to address this issue due to its automation and ease of operation. Nevertheless, automated C. elegans sorting with multiple parameters requires efficient identification technology due to the different research demands for worm phenotypes. To improve the efficiency and accuracy of multi-parameter sorting, we developed a deep learning model using You Only Look Once (YOLO)v7 to detect and recognize C. elegans automatically. We used a dataset of 3931 annotated worms in microfluidic chips from various studies. Our model showed higher precision in automated C. elegans identification than YOLOv5 and Faster R-CNN, achieving a mean average precision (mAP) at a 0.5 intersection over a union (mAP@0.5) threshold of 99.56%. Additionally, our model demonstrated good generalization ability, achieving an mAP@0.5 of 94.21% on an external validation set. Our model can efficiently and accurately identify and calculate multiple phenotypes of worms, including size, movement speed, and fluorescence. The multi-parameter identification model can improve sorting efficiency and potentially promote the development of automated and integrated microfluidic platforms.

Microfluidic-Assisted Caenorhabditis elegans Sorting: Current Status and Future Prospects

Caenorhabditis elegans (C. elegans) has been a popular model organism for several decades since its first discovery of the huge research potential for modeling human diseases and genetics. Sorting is an important means of providing stage- or age-synchronized worm populations for many worm-based bioassays. However, conventional manual techniques for C. elegans sorting are tedious and inefficient, and commercial complex object parametric analyzer and sorter is too expensive and bulky for most laboratories. Recently, the development of lab-on-a-chip (microfluidics) technology has greatly facilitated C. elegans studies where large numbers of synchronized worm populations are required and advances of new designs, mechanisms, and automation algorithms. Most previous reviews have focused on the development of microfluidic devices but lacked the summaries and discussion of the biological research demands of C. elegans, and are hard to read for worm researchers. We aim to comprehensively review the up-to-date microfluidic-assisted C. elegans sorting developments from several angles to suit different background researchers, i.e., biologists and engineers. First, we highlighted the microfluidic C. elegans sorting devices' advantages and limitations compared to the conventional commercialized worm sorting tools. Second, to benefit the engineers, we reviewed the current devices from the perspectives of active or passive sorting, sorting strategies, target populations, and sorting criteria. Third, to benefit the biologists, we reviewed the contributions of sorting to biological research. We expect, by providing this comprehensive review, that each researcher from this multidisciplinary community can effectively find the needed information and, in turn, facilitate future research.

Long-Term Culture of Individual Caenorhabditis elegans on Solid Media for Longitudinal Fluorescence Monitoring and Aversive Interventions

Caenorhabditis elegans are widely used to study aging biology. The standard practice in C. elegans aging studies is to culture groups of worms on solid nematode growth media (NGM), allowing the efficient collection of population-level data for survival and other physiological phenotypes, and periodic sampling of subpopulations for fluorescent biomarker quantification. Limitations to this approach are the inability to (1) follow individual worms over time to develop age trajectories for phenotypes of interest and (2) monitor fluorescent biomarkers directly in the context of the culture environment. Alternative culture approaches use liquid culture or microfluidics to monitor individual animals over time, in some cases including fluorescence quantification, with the tradeoff that the culture environment is contextually distinct from solid NGM. The WorMotel is a previously described microfabricated multi-well device for culturing isolated worms on solid NGM. Each worm is maintained in a well containing solid NGM surrounded by a moat filled with copper sulfate, a contact repellent for C. elegans, allowing longitudinal monitoring of individual animals. We find copper sulfate insufficient to prevent worms from fleeing when subjected to aversive interventions common in aging research, including dietary restriction, pathogenic bacteria, and chemical agents that induce cellular stress. The multi-well devices are also molded from polydimethylsiloxane, which produces high background artifacts in fluorescence imaging. This protocol describes a new approach for culturing isolated roundworms on solid NGM using commercially available polystyrene microtrays, originally designed for human leukocyte antigen (HLA) typing, allowing the measurement of survival, physiological phenotypes, and fluorescence across the lifespan. A palmitic acid barrier prevents worms from fleeing, even in the presence of aversive conditions. Each plate can culture up to 96 animals and easily adapts to a variety of conditions, including dietary restriction, RNAi, and chemical additives, and is compatible with automated systems for collecting lifespan and activity data.

Dicarbonyl/L-xylulose reductase (DCXR) producing xylitol regulates egg retention through osmolality control in Caenorhabditis elegans

To support life, the osmolality of the cellular fluid is tightly regulated by various means, including osmolyte control. Dicarbonyl/L-xylulose reductase (DCXR) is a highly conserved enzyme reducing L-xylulose to xylitol, which serves as an effective osmolyte in various mammalian and human tissues such as lung epithelium, sperm, and lens. DHS-21 is the only DCXR ortholog in Caenorhabditis elegans, and DCXR null mutant worms accumulate eggs in the uterus. However, it has been unknown how and why the mutant worms impair egg retention. In this study, we tested whether the egg-retention in dhs-21 (jh129), the DCXR null mutant worm, is sensitive to changes in osmolarity. Low osmolality reverted the egg retention phenotype of dhs-21(jh129), while high osmolarity aggravated it. Also, knock-down of either one of osr-1, osm-7, or osm-11, osmoregulatory genes, also rescued egg-retention phenotypes of the null mutants. The study indicates that DCXR functions in fluid homeostasis by regulating cellular osmolality in C. elegans and provides insights into DCXR-involved clinical conditions, such as congenital cataracts and malfunctioning lung and kidney.

Microfluidic Devices for Behavioral Analysis, Microscopy, and Neuronal Imaging in Caenorhabditis elegans

Microfluidic devices offer several advantages for C. elegans research, particularly for presenting precise physical and chemical environments, immobilizing animals during imaging, quantifying behavior, and automating screens. However, challenges to their widespread adoption in the field include increased complexity over conventional methods, operational problems (such as clogging, leaks, and bubbles), difficulty in obtaining or fabricating devices, and the need to characterize biological results obtained from new assay formats. Here we describe the preparation and operation of simple, reusable microfluidic devices for quantifying behavioral responses to chemical patterns, and single-use devices to arrange animals for time-lapse microscopy and to measure neuronal activity. We focus on details that eliminate or reduce the frustrations commonly experienced by new users of microfluidic devices.

Morphological Characterization of small, dumpy, and long Phenotypes in Caenorhabditis elegans

The determinant factors of an organism's size during animal development have been explored from various angles but remain partially understood. In Caenorhabditis elegans, many genes affecting cuticle structure, cell growth, and proliferation have been identified to regulate the worm's overall morphology, including body size. While various mutations in those genes directly result in changes in the morphological phenotypes, there is still a need for established, clear, and distinct standards to determine the apparent abnormality in a worm's size and shape. In this study, we measured the body length, body width, terminal bulb length, and head size of mutant worms with reported Dumpy (Dpy), Small (Sma) or Long (Lon) phenotypes by plotting and comparing their respective ratios of various parameters. These results show that the Sma phenotypes are proportionally smaller overall with mild stoutness, and Dpy phenotypes are significantly stouter and have disproportionally small head size. This study provides a standard platform for determining morphological phenotypes designating and annotating mutants that exhibit body shape variations, defining the morphological phenotype of previously unexamined mutants.