A size threshold governs Caenorhabditis elegans developmental progression

Maintenance of appropriate size scaling of the C. elegans pharynx by YAP-1

Even slight imbalance between the growth rate of different organs can accumulate to a large deviation from their appropriate size during development. Here, we use live imaging of the pharynx of C. elegans to ask if and how organ size scaling nevertheless remains uniform among individuals. Growth trajectories of hundreds of individuals reveal that pharynxes grow by a near constant volume per larval stage that is independent of their initial size, such that undersized pharynxes catch-up in size during development. Tissue-specific depletion of RAGA-1, an activator of mTOR and growth, shows that maintaining correct pharynx-to-body size proportions involves a bi-directional coupling between pharynx size and body growth. In simulations, this coupling cannot be explained by limitation of food uptake alone, and genetic experiments reveal an involvement of the mechanotransducing transcriptional co-regulator yap-1. Our data suggests that mechanotransduction coordinates pharynx growth with other tissues, ensuring body plan uniformity among individuals.

Periods of environmental sensitivity couple larval behavior and development

The typical life cycle in most animal phyla includes a larval period that bridges embryogenesis and adulthood1. Despite the great diversity of larval forms, all larvae grow, acquire adult morphology and function, while navigating their habitats to obtain resources necessary for development. How larval development is coordinated with behavior remains substantially unclear. Here, we describe features of the iterative organization of larval stages that serve to assess the environment and procure resources prior to costly developmental commitments. We found that male-excreted pheromones accelerate2-4 the onset of adulthood in C. elegans hermaphrodites by coordinately advancing multiple developmental events and growth during the last larval stage. The larvae are sensitive to the accelerating male pheromones only at the end of the penultimate larval stage, just before the acceleration begins. Other larval stages also contain windows of sensitivity to environmental inputs. Importantly, behaviors associated with search and consumption of food are distinct between early and late portions of larval stages. We infer that each larval stage in C. elegans is subdivided into two epochs: A) global assessment of the environment to identify the most suitable patch and B) consumption of sufficient food and acquisition of salient information for developmental events in the next stage. We predict that in larvae of other species behavior is also divided into distinct epochs optimized either for assessing the habitat or obtaining the resources. Thus, a major role of larval behavior is to coordinate the orderly progression of development in variable environments.

Diet can alter the cost of resistance to a natural parasite in Caenorhabditis elegans

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.

Size adjustment occurs during the larval growth of the separated blastomeres of the starfish, Patiria Pectinifera

Starfish embryos derived from blastomeres separated at the early cleavage stage exhibit morphogenesis to form normally shaped, but smaller-sized dwarf bipinnaria larvae. To further understand this developmental capacity, we primarily characterized the morphogenetic processes of separated 2-cell and 4-cell stage blastomeres during the embryonic and larval periods of the starfish, Patiria Pectinifera. Using non-separated blastomeres as the control, we subjected the separated blastomeres to morphological analyses in conjunction with quantitative measurements of the changes in their body sizes with time post-fertilization. Our results were as follows: (i) Blastomeres separated at 2-cell and 4-cell stages synchronously developed into dwarf-sized bipinnaria larvae. (ii) Upon reaching a body size of 500-700 μm, all the bipinnaria larvae originating from the separated blastomeres and controls began to undergo a series of similar organ formation events in preparation for metamorphosis-recognized as the demarcation between the early and late substages of the bipinnaria larval period. (iii) The separated blastomeres became brachiolaria larvae capable of undergoing metamorphosis at differing rates after reaching approximately 1000-1200 μm body sizes, with adult rudiment and sensory organ forming functionally. (iv) The unfed controls and dwarf bipinnaria larvae derived from blastomeres separated at the 4-cell stage arrested their development synchronously without reaching the threshold size required for the latter half of the bipinnaria stage. These results, taken together, suggested that separated blastomeres possess the developmental capacity to become brachiolaria larvae through a shift in morphogenetic regulation from a synchronous growth to size adjustment during the larval period.

Transgenerational effects of alcohol on behavioral sensitivity to alcohol in Caenorhabditis elegans

Alcohol abuse and dependence have a substantial heritable component. Although the genome has been considered the sole vehicle of heritable phenotypes, recent studies suggest that drug or alcohol exposure may induce alterations in gene expression that are transmitted across generations. Still, the transgenerational impact of alcohol use (and abuse) remains largely unexplored in part because multigenerational studies using rodent models present challenges for time, sample size, and genetic heterogeneity. Here, we took advantage of the extremely short generation time, large broods, and clonal form of reproduction of the nematode Caenorhabditis elegans. We developed a model of pre-fertilization parental alcohol exposure to test alterations in behavioral responses to acute alcohol treatment (referred to in short as intoxication) in subsequent F1, F2 and F3 generations. We found that chronic and intermittent alcohol-treatment paradigms resulted in opposite changes to intoxication sensitivity of F3 progeny that were only apparent when controlling for yoked trials. Chronic alcohol-treatment paradigm in the parental generation resulted in alcohol-naïve F3 progeny displaying moderate resistance to intoxication. Intermittent treatment resulted in alcohol-naïve F3 progeny displaying moderate hypersensitivity to intoxication. Further study of these phenomena using this new C. elegans model may yield mechanistic insights into how transgenerational effects may occur in other animals.

Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces

Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also highly expressed when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worm's Toll-like innate immunity pathway and several immune effectors (e.g., bactericidal/permeability-increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires the oxidative phosphorylation and reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development.

Coupling of growth rate and developmental tempo reduces body size heterogeneity in C. elegans

Animals increase by orders of magnitude in volume during development. Therefore, small variations in growth rates among individuals could amplify to a large heterogeneity in size. By live imaging of C. elegans, we show that amplification of size heterogeneity is prevented by an inverse coupling of the volume growth rate to the duration of larval stages and does not involve strict size thresholds for larval moulting. We perturb this coupling by changing the developmental tempo through manipulation of a transcriptional oscillator that controls the duration of larval development. As predicted by a mathematical model, this perturbation alters the body volume. Model analysis shows that an inverse relation between the period length and the growth rate is an intrinsic property of genetic oscillators and can occur independently of additional complex regulation. This property of genetic oscillators suggests a parsimonious mechanism that counteracts the amplification of size differences among individuals during development.

Animals must reach the correct size during development, despite stochastic differences in their growth rate. Here, Stojanovski et al. show that a coupling of growth and development by an oscillatory timer buffers fluctuations in the growth of the nematode C. elegans to ensure its correct size.

Deviations from temporal scaling support a stage-specific regulation for C. elegans postembryonic development

Background

After embryonic development, Caenorhabditis elegans progress through for larval stages, each of them finishing with molting. The repetitive nature of C. elegans postembryonic development is considered an oscillatory process, a concept that has gained traction from regulation by a circadian clock gene homologue. Nevertheless, each larval stage has a defined duration and entails specific events. Since the overall duration of development is controlled by numerous factors, we have asked whether different rate-limiting interventions impact all stages equally.

Results

We have measured the duration of each stage of development for over 2500 larvae, under varied environmental conditions known to alter overall developmental rate. We applied changes in temperature and in the quantity and quality of nutrition and analysed the effect of genetically reduced insulin signalling. Our results show that the distinct developmental stages respond differently to these perturbations. The changes in the duration of specific larval stages seem to depend on stage-specific events. Furthermore, our high-resolution measurement of the effect of temperature on the stage-specific duration of development has unveiled novel features of temperature dependence in C. elegans postembryonic development.

Conclusions

Altogether, our results show that multiple factors fine tune developmental timing, impacting larval stages independently. Further understanding of the regulation of this process will allow modelling the mechanisms that control developmental timing.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01295-2.

Temporal scaling in C. elegans larval development

An enduring mystery of development is how its timing is controlled, particularly for development after birth, where timing is highly flexible and depends on environmental conditions, such as food availability and diet. We followed timing of cell- and organism-level events in individual Caenorhabditis elegans larvae developing from hatching to adulthood, uncovering widespread variations in event timing, both between isogenic individuals in the same environment and when changing conditions and genotypes. However, in almost all cases, we found that events occurred at the same time, when time was rescaled by the duration of development measured in each individual. This observation of “temporal scaling” poses strong constraints on models to explain timing of larval development.

It is essential that correct temporal order of cellular events is maintained during animal development. During postembryonic development, the rate of development depends on external conditions, such as food availability, diet, and temperature. How timing of cellular events is impacted when the rate of development is changed at the organism level is not known. We used a unique time-lapse microscopy approach to simultaneously measure timing of oscillatory gene expression, hypodermal stem cell divisions, and cuticle shedding in individual Caenorhabditis elegans larvae, as they developed from hatching to adulthood. This revealed strong variability in timing between isogenic individuals under the same conditions. However, this variability obeyed “temporal scaling,” meaning that events occurred at the same time when measured relative to the total duration of development in each individual. We also observed pervasive changes in timing when temperature, diet, or genotype were varied, but with larval development divided in “epochs” that differed in how event timing was impacted. Yet, these variations in timing were still explained by temporal scaling when time was rescaled by the duration of the respective epochs in each individual. Surprisingly, timing obeyed temporal scaling even in mutants lacking lin-42/Period, presumed a core regulator of timing of larval development, that exhibited strongly delayed, heterogeneous timing. However, shifting conditions middevelopment perturbed temporal scaling and changed event order in a highly condition-specific manner, indicating that a complex machinery is responsible for temporal scaling under constant conditions.

Reciprocal interactions between transforming growth factor beta signaling and collagens: Insights from Caenorhabditis elegans

Studies in genetically tractable organisms such as the nematode Caenorhabditis elegans have led to pioneering insights into conserved developmental regulatory mechanisms. For example, Smad signal transducers for the transforming growth factor beta (TGF-β) superfamily were first identified in C. elegans and in the fruit fly Drosophila. Recent studies of TGF-β signaling and the extracellular matrix (ECM) in C. elegans have forged unexpected links between signaling and the ECM, yielding novel insights into the reciprocal interactions that occur across tissues and spatial scales, and potentially providing new opportunities for the study of biomechanical regulation of gene expression.

Inferring temporal organization of postembryonic development from high-content behavioral tracking

Understanding temporal regulation of development remains an important challenge. Whereas average, species-typical timing of many developmental processes has been established, less is known about inter-individual variability and correlations in timing of specific events. We addressed these questions in the context of postembryonic development in Caenorhabditis elegans. Based on patterns of locomotor activity of freely moving animals, we inferred durations of four larval stages (L1-L4) in over 100 individuals. Analysis of these data supports several conclusions. Individuals have consistently faster or slower rates of development because durations of L1 through L3 stages are positively correlated. The last larval stage, the L4, is less variable than the earlier stages and its duration is largely independent of the rate of early larval development, implying existence of two distinct larval epochs. We describe characteristic patterns of variation and correlation, as well as the fact that stage durations tend to scale relative to total developmental time. This scaling relationship suggests that each larval stage is not limited by an absolute duration, but is instead terminated when a subset of events that must occur prior to adulthood have been completed. The approach described here offers a scalable platform that will facilitate the study of temporal regulation of postembryonic development.

SID-2 negatively regulates development likely independent of nutritional dsRNA uptake

RNA interference (RNAi) is a gene regulatory mechanism based on RNA-RNA interaction conserved through eukaryotes. Surprisingly, many animals can take-up human-made double stranded RNA (dsRNA) from the environment to initiate RNAi suggesting a mechanism for dsRNA-based information exchange between organisms and their environment. However, no naturally occurring example has been identified since the discovery of the phenomenon 22 years ago. Therefore it remains enigmatic why animals are able to take up dsRNA. Here, we explore other possible functions by performing phenotypic studies of dsRNA uptake deficient sid-2 mutants in Caenorhabditis elegans. We find that SID-2 does not have a nutritional role in feeding experiments using genetic sensitized mutants. Furthermore, we use robot assisted imaging to show that sid-2 mutants accelerate growth rate and, by maternal contribution, body length at hatching. Finally, we perform transcriptome and lipidome analysis showing that sid-2 has no effect on energy storage lipids, but affects signalling lipids and the embryo transcriptome. Overall, these results suggest that sid-2 has mild effects on development and is unlikely functioning in the nutritional uptake of dsRNA. These findings broaden our understanding of the biological role of SID-2 and motivate studies identifying the role of environmental dsRNA uptake.

Epidermal PAR-6 and PKC-3 are essential for larval development of C. elegans and organize non-centrosomal microtubules

The cortical polarity regulators PAR-6, PKC-3, and PAR-3 are essential for the polarization of a broad variety of cell types in multicellular animals. In C. elegans, the roles of the PAR proteins in embryonic development have been extensively studied, yet little is known about their functions during larval development. Using inducible protein degradation, we show that PAR-6 and PKC-3, but not PAR-3, are essential for postembryonic development. PAR-6 and PKC-3 are required in the epidermal epithelium for animal growth, molting, and the proper pattern of seam-cell divisions. Finally, we uncovered a novel role for PAR-6 in organizing non-centrosomal microtubule arrays in the epidermis. PAR-6 was required for the localization of the microtubule organizer NOCA-1/Ninein, and defects in a noca-1 mutant are highly similar to those caused by epidermal PAR-6 depletion. As NOCA-1 physically interacts with PAR-6, we propose that PAR-6 promotes non-centrosomal microtubule organization through localization of NOCA-1/Ninein.

Nutritional control of postembryonic development progression and arrest in Caenorhabditis elegans

Developmental programs are under strict genetic control that favors robustness of the process. In order to guarantee the same outcome in different environmental situations, development is modulated by input pathways, which inform about external conditions. In the nematode Caenorhabditis elegans, the process of postembryonic development involves a series of stereotypic cell divisions, the progression of which is controlled by the nutritional status of the animal. C. elegans can arrest development at different larval stages, leading to cell arrest of the relevant divisions of the stage. This means that studying the nutritional control of development in C. elegans we can learn about the mechanisms controlling cell division in an in vivo model. In this work, we reviewed the current knowledge about the nutrient sensing pathways that control the progression or arrest of development in response to nutrient availability, with a special focus on the arrest at the L1 stage.

Fluorescence-based sorting of Caenorhabditis elegans via acoustofluidics

Effectively isolating and categorizing large quantities of Caenorhabditis elegans (C. elegans) based on different phenotypes is important for most worm research, especially genetics. Here we present an integrated acoustofluidic chip capable of identifying worms of interest based on expression of a fluorescent protein in a continuous flow and then separate them accordingly in a high-throughput manner. Utilizing planar fiber optics as the detection unit, our acoustofluidic device requires no temporary immobilization of worms for interrogation/detection, thereby improving the throughput. Implementing surface acoustic waves (SAW) as the sorting unit, our device provides a contact-free method to move worms of interest to the desired outlet, thus ensuring the biocompatibility for our chip. Our device can sort worms of different developmental stages (L3 and L4 stage worms) at high throughput and accuracy. For example, L3 worms can be processed at a throughput of around 70 worms per min with a sample purity over 99%, which remains over 90% when the throughput is increased to around 115 worms per min. In our acoustofluidic chip, the time period to complete the detection and sorting of one worm is only 50 ms, which outperforms nearly all existing microfluidics-based worm sorting devices and may be further reduced to achieve higher throughput.

A new method for measuring the size of nematodes using image processing

Many studies have been made on nematodes, especially Caenorhabditis Elegans, which are used as a model organism. In many studies, the size of the nematode is important. This article describes a method of measuring the length, volume and surface area of nematodes from photographs. The method uses the imaging software ImageJ, which is in the public domain. Two macros are described. The first converts the images into binary form, and the second uses several built-in functions to measure the length of the worm and its diameter along its length. If it is assumed that the worm has a circular cross-section, then the volume and surface area of the nematode can be calculated. This is a cheap and easy technique.

Oxygen consumption rate of Caenorhabditis elegans as a high-throughput endpoint of toxicity testing using the Seahorse XFe96 Extracellular Flux Analyzer

Caenorhabditis elegans presents functioning, biologically relevant phenotypes and is frequently used as a bioindicator of toxicity. However, most C. elegans in vivo effect-assessment methods are laborious and time consuming. Therefore, we developed a novel method to measure the oxygen consumption rate of C. elegans as a sublethal endpoint of toxicity. This protocol was tested by exposing 50 larval stage one C. elegans individuals for 48 h (at 20 °C) to different concentrations of two toxicants i.e. benzylcetyldimethylammonium chloride (BAC-C16) and cadmium (Cd). Following exposures, the oxygen consumption rate of the C. elegans individuals were measured using the high-throughput functionality of the Seahorse XFe96 Extracellular Flux Analyzer. Dose-response curves for BAC-C16 (R2 = 0.93; P = 0.001) and Cd (R2 = 0.98; P = 0.001) were created. Furthermore, a strong, positive correlation was evidenced between C. elegans oxygen consumption rate and a commonly used, ecologically relevant endpoint of toxicity (growth inhibition) for BAC-C16 (R2 = 0.93; P = 0.0001) and Cd (R2 = 0.91; P = 0.0001). The data presented in this study show that C. elegans oxygen consumption rate can be used as a promising functional measurement of toxicity.

The Detection of Early Epigenetic Inheritance of Mitochondrial Stress in C. Elegans with a Microfluidic Phenotyping Platform

Fluctuations and deterioration in environmental conditions potentially have a phenotypic impact that extends over generations. Transgenerational epigenetics is the defined term for such intergenerational transient inheritance without an alteration in the DNA sequence. The model organism Caenorhabditis elegans is exceptionally valuable to address transgenerational epigenetics due to its short lifespan, well-mapped genome and hermaphrodite behavior. While the majority of the transgenerational epigenetics on the nematodes focuses on generations-wide heritage, short-term and in-depth analysis of this phenomenon in a well-controlled manner has been lacking. Here, we present a novel microfluidic platform to observe mother-to-progeny heritable transmission in C. elegans at high imaging resolution, under significant automation, and enabling parallelized studies. After approximately 24 hours of culture of L4 larvae under various concentrations and application periods of doxycycline, we investigated if mitochondrial stress was transferred from the mother nematodes to the early progenies. Automated and custom phenotyping algorithms revealed that a minimum doxycycline concentration of 30 µg/mL and a drug exposure time of 15 hours applied to the mothers could induce mitochondrial stress in first embryo progenies indeed, while this inheritance was not clearly observed later in L1 progenies. We believe that our new device could find further usage in transgenerational epigenetic studies modeled on C. elegans.

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

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.

Automated Platform for Long-Term Culture and High-Content Phenotyping of Single C. elegans Worms

The nematode Caenorhabditis elegans is a suitable model organism in drug screening. Traditionally worms are grown on agar plates, posing many challenges for long-term culture and phenotyping of animals under identical conditions. Microfluidics allows for 'personalized' phenotyping, as microfluidic chips permit collecting individual responses over worms' full life. Here, we present a multiplexed, high-throughput, high-resolution microfluidic approach to culture C. elegans from embryo to the adult stage at single animal resolution. We allocated single embryos to growth chambers, for observing the main embryonic and post-embryonic development stages and phenotypes, while exposing worms to up to 8 different well-controlled chemical conditions. Our approach allowed eliminating bacteria aggregation and biofilm formation-related clogging issues, which enabled us performing up to 80 hours of automated single worm culture studies. Our microfluidic platform is linked with an automated phenotyping code that registers organism-associated phenotypes at high-throughput. We validated our platform with a dose-response study of the anthelmintic drug tetramisole by studying its influence through the life cycle of the nematodes. In parallel, we could observe development effects and variations in single embryo and worm viability due to the bleaching procedure that is standardly used for harvesting the embryos from a worm culture agar plate.

Automated high-content phenotyping from the first larval stage till the onset of adulthood of the nematode Caenorhabditis elegans

The nematode Caenorhabditis elegans is increasingly used as a model for human biology. However, in vivo culturing platforms for C. elegans allowing high-content phenotyping during their life cycle in an automated fashion are lacking so far. Here, a multiplexed microfluidic platform for the rapid high-content phenotyping of populations of C. elegans down to single animal resolution is presented. Nematodes are (i) reversibly and regularly confined during their life inside tapered channels for imaging fluorescence signal expression and to measure their growth parameters, and (ii) allowed to freely move in microfluidic chambers, during which the swimming behavior was video-recorded. The obtained data sets are analyzed in an automated way and 19 phenotypic parameters are extracted. Our platform is employed for studying the effect of bacteria dilution, a form of dietary restriction (DR) in nematodes, on a worm model of Huntington's disease and demonstrates the influence of DR on disease regression.

Recent Advances and Trends in Microfluidic Platforms for C. elegans Biological Assays

Microfluidics has proven to be a key tool in quantitative biological research. The C. elegans research community in particular has developed a variety of microfluidic platforms to investigate sensory systems, development, aging, and physiology of the nematode. Critical for the growth of this field, however, has been the implementation of concurrent advanced microscopy, hardware, and software technologies that enable the discovery of novel biology. In this review, we highlight recent innovations in microfluidic platforms used for assaying C. elegans and discuss the novel technological approaches and analytic strategies required for these systems. We conclude that platforms that provide analytical frameworks for assaying specific biological mechanisms and those that take full advantage of integrated technologies to extract high-value quantitative information from worm assays are most likely to move the field forward.

Hierarchical Size Scaling during Multicellular Growth and Development

Multicellular organisms must regulate their growth across the diverse length scales of biological organization, but how this growth is controlled from organelle to body, while coordinating interdependent functions at each scale, remains poorly understood. We utilized the C. elegans worm intestine as a model system to identify distinct allometric scaling laws, revealing that the growth of individual structures is differentially regulated during development. We show that the volume of the nucleolus, a subcellular organelle, is directly proportional (isometric) to cell size during larval development. In contrast to findings in a variety of other systems, the size of the nucleus grows more slowly and is hypoallometric to the cell. We further demonstrate that the relative size of the nucleolus, the site of ribosome biogenesis, is predictive of the growth rate of the entire worm. These results highlight the importance of subcellular size for organism-level function in multicellular organisms.

Microfluidic systems for high-throughput and high-content screening using the nematode Caenorhabditis elegans

In a typical high-throughput drug screening (HTS) process, up to millions of chemical compounds are applied to cells cultured in well plates, aiming to find molecules that exhibit a robust dose-response, as evidenced for example by a fluorescence signal. In high-content screening (HCS), one goes a step further by linking the tested compounds to phenotypic information, obtained, for instance, from microscopic cell images, thereby creating richer data sets that also require more advanced analysis methods. The nematode Caenorhabditis elegans came into the screening picture due to the wide availability of its mutants and human disease models, its relatively easy culture and short life cycle. Being a whole-organism model, it allows drug testing under physiological conditions at multi-tissue levels and provides additional observable phenotypes with respect to cell models, related, for instance, to development, aging, behavior or motility. Worm-based HTS studies in liquid environments on microwell plates have been demonstrated, while microfluidic devices allowed surpassing the performance of plates by enabling more versatile and accurate assays, precise and dynamic dosing of compounds, and readouts down to single-animal resolution. In this review, we discuss microfluidic devices for C. elegans analysis and related studies, published in the period from 2012 to 2017. After an introduction to the different screening approaches, we first focus on microfluidic systems with potential for screening applications. Various enabling technologies, e.g. electrophysiological on-chip recordings or laser axotomy, have been implemented, as well as techniques for reversible worm immobilization and high-resolution imaging, combined with algorithms for automated experimentation and analysis. Several devices for developmental or behavioral assays, and worm sorting based on different phenotypes, have been proposed too. In a subsequent section, we review the application of microfluidic-based systems for medium- and high-throughput screens, including neurobiology and neurodegeneration studies, aging and developmental assays, toxicity and pathogenesis screens, as well as behavioral and motility assays. A thorough analysis of this work reveals a trend towards microfluidic systems more and more capable of offering high-quality analyses of large worm populations, based on multi-phenotypic and/or longitudinal readouts, with clear potential for their application in larger HTS/HCS contexts.

A simple culture system for long-term imaging of individual C. elegans

We have miniaturized standard culture techniques to rear arrays of isolated, individual C. elegans throughout their lives on solid gel media. The resulting apparatus is compatible with brightfield and fluorescence microscopy, enabling longitudinal studies of morphology and fluorescent transgene expression. Our culture system exploits a novel crosslinking reaction between a polyethylene glycol hydrogel and a silicone elastomer to constrain animals to individual "corrals" on the gel surface. These devices are simple to construct on the benchtop with commercially available reagents, and, unlike microfluidic isolation methods, do not rely on micropatterned materials. We demonstrate that this new culture method has negligible effects on the physiology of C. elegans compared to standard culture on agar plates. In addition, RNAi techniques are effective in this system. Finally, the hydrogel-silicone binding chemistry that we developed also allows traditional microfluidic devices to be covalently attached to gel substrates instead of glass.

Microfluidic platform with spatiotemporally controlled micro-environment for studying long-term C. elegans developmental arrests

Animals' long-term survival is dependent on their ability to sense, filter and respond to their environment at multiple timescales. For example, during development, animals integrate environmental information, which can then modulate adult behavior and developmental trajectory. The neural and molecular mechanisms that underlie these changes are poorly understood. C. elegans is a powerful model organism to study such mechanisms; however, conventional plate-based culturing techniques are limited in their ability to consistently control and modulate an animal's environmental conditions. To address this need, we developed a microfluidics-based experimental platform capable of long-term culture of populations of developing C. elegans covering the L1 larval stage to adulthood, while achieving spatial consistency and temporal control of their environment. To prevent bacterial accumulation and maintain optimal flow characteristics and nutrient consistency over the operational period of over one hundred and fifty hours, several features of the microfluidic system and the peripheral equipment were optimized. By manipulating food and pheromone exposure over several days, we were able to demonstrate environmental-dependent changes to growth rate and entry to dauer, an alternative developmental state. We envision this system to be useful in studying the mechanisms underlying long timescale changes to behavior and development in response to environmental changes.

High-throughput screening in the C. elegans nervous system

The nematode Caenorhabditis elegans is widely used as a model organism in the field of neurobiology. The wiring of the C. elegans nervous system has been entirely mapped, and the animal's optical transparency allows for in vivo observation of neuronal activity. The nematode is also small in size, self-fertilizing, and inexpensive to cultivate and maintain, greatly lending to its utility as a whole-animal model for high-throughput screening (HTS) in the nervous system. However, the use of this organism in large-scale screens presents unique technical challenges, including reversible immobilization of the animal, parallel single-animal culture and containment, automation of laser surgery, and high-throughput image acquisition and phenotyping. These obstacles require significant modification of existing techniques and the creation of new C. elegans-based HTS platforms. In this review, we outline these challenges in detail and survey the novel technologies and methods that have been developed to address them.

Long-term time-lapse microscopy of C. elegans post-embryonic development

We present a microscopy technique that enables long-term time-lapse microscopy at single-cell resolution in moving and feeding Caenorhabditis elegans larvae. Time-lapse microscopy of C. elegans post-embryonic development is challenging, as larvae are highly motile. Moreover, immobilization generally leads to rapid developmental arrest. Instead, we confine larval movement to microchambers that contain bacteria as food, and use fast image acquisition and image analysis to follow the dynamics of cells inside individual larvae, as they move within each microchamber. This allows us to perform fluorescence microscopy of 10-20 animals in parallel with 20 min time resolution. We demonstrate the power of our approach by analysing the dynamics of cell division, cell migration and gene expression over the full ∼48 h of development from larva to adult. Our approach now makes it possible to study the behaviour of individual cells inside the body of a feeding and growing animal.