An automated microfluidic platform for C. elegans embryo arraying, phenotyping, and long-term live imaging

Advanced Neural Functional Imaging in C. elegans Using Lab-on-a-Chip Technology

The ability to perceive and adapt to environmental changes is crucial for the survival of all organisms. Neural functional imaging, particularly in model organisms, such as Caenorhabditis elegans, provides valuable insights into how animals sense and process external cues through their nervous systems. Because of its fully mapped neural anatomy, transparent body, and genetic tractability, C. elegans serves as an ideal model for these studies. This review focuses on advanced methods for neural functional imaging in C. elegans, highlighting calcium imaging techniques, lab-on-a-chip technologies, and their applications in the study of various sensory modalities, including chemosensation, mechanosensation, thermosensation, photosensation, and magnetosensation. We discuss the benefits of these methods in terms of precision, reproducibility, and ability to study dynamic neural processes in real time, ultimately advancing our understanding of the fundamental principles of neural activity and connectivity.

Novel 18-norspirostane steroidal saponins: Extending lifespan and mitigating neurodegeneration through promotion of mitophagy and mitochondrial biogenesis in Caenorhabditis elegans

Pharmacological strategies to delay aging and combat age-related diseases are increasingly promising. This study explores the anti-aging and therapeutic effects of two novel 18-norspirostane steroidal saponins from Trillium tschonoskii Maxim, namely deoxytrillenoside CA (DTCA) and epitrillenoside CA (ETCA), using Caenorhabditis elegans (C. elegans). Both DTCA and ETCA significantly extended the lifespan of wild-type N2 worms and improved various age-related phenotypes, including muscle health, motility, pumping rate, and lipofuscin accumulation. Furthermore, these compounds exhibited notable alleviation of pathology associated with Parkinson's disease (PD) and Huntington's disease (HD), such as the reduction of α-synuclein and poly40 aggregates, improvement in motor deficits, and mitigation of neuronal damage. Meanwhile, DTCA and ETCA improved the lifespan and healthspan of PD- and HD-like C. elegans models. Additionally, DTCA and ETCA enhanced the resilience of C. elegans against heat and oxidative stress challenges. Mechanistic studies elucidated that DTCA and ETCA induced mitophagy and promoted mitochondrial biogenesis in C. elegans, while genetic mutations or RNAi knockdown affecting mitophagy and mitochondrial biogenesis effectively eliminated their capacity to extend lifespan and reduce pathological protein aggregates. Together, these compelling findings highlight the potential of DTCA and ETCA as promising therapeutic interventions for delaying aging and preventing age-related diseases.

Contractile ring composition dictates kinetics of in silico contractility

Constriction kinetics of the cytokinetic ring are expected to depend on dynamic adjustment of contractile ring composition, but the impact of ring component abundance dynamics on ring constriction is understudied. Computational models generally assume that contractile networks maintain constant total amounts of components, which is not always true. To test how compositional dynamics affect constriction kinetics, we first measured F-actin, non-muscle myosin II, septin, and anillin during Caenorhabditis elegans zygotic mitosis. A custom microfluidic device that positioned the cell with the division plane parallel to a light sheet allowed even illumination of the cytokinetic ring. Measured component abundances were implemented in a three-dimensional agent-based model of a membrane-associated contractile ring. With constant network component amounts, constriction completed with biologically unrealistic kinetics. However, imposing the measured changes in component quantities allowed this model to elicit realistic constriction kinetics. Simulated networks were more sensitive to changes in motor and filament amounts than those of crosslinkers and tethers. Our findings highlight the importance of network composition for actomyosin contraction kinetics.

CeLab, a microfluidic platform for the study of life history traits, reveals metformin and SGK-1 regulation of longevity and reproductive span

The potential to carry out high-throughput assays in a whole organism in a small space is one of the benefits of C. elegans, but worm assays often require a large sample size with frequent physical manipulations, rendering them highly labor-intensive. Microfluidic assays have been designed with specific questions in mind, such as analysis of behavior, embryonic development, lifespan, and motility. While these devices have many advantages, current technologies to automate worm experiments have several limitations that prevent widespread adoption, and most do not allow analyses of reproduction-linked traits. We developed a miniature C. elegans lab-on-a-chip device, CeLab, a reusable, multi-layer device with 200 separate incubation arenas that allows progeny removal, to automate a variety of worm assays on both individual and population levels. CeLab enables high-throughput simultaneous analysis of lifespan, reproductive span, and progeny production, refuting assumptions about the disposable soma hypothesis. Because CeLab chambers require small volumes, the chip is ideal for drug screens; we found that drugs previously shown to increase lifespan also increase reproductive span, and we discovered that low-dose metformin increases both. CeLab reduces the limitations of escaping and matricide that typically limit plate assays, revealing that feeding with heat-killed bacteria greatly extends lifespan and reproductive span of mated animals. CeLab allows tracking of life history traits of individuals, which revealed that the nutrient-sensing mTOR pathway mutant, sgk-1, reproduces nearly until its death. These findings would not have been possible to make in standard plate assays, in low-throughput assays, or in normal population assays.

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.

A spiral microfluidic device for rapid sorting, trapping, and long-term live imaging of Caenorhabditis elegans embryos

Caenorhabditis elegans embryos have been widely used to study cellular processes and developmental regulation at early stages. However, most existing microfluidic devices focus on the studies of larval or adult worms rather than embryos. To accurately study the real-time dynamics of embryonic development under different conditions, many technical barriers must be overcome; these can include single-embryo sorting and immobilization, precise control of the experimental environment, and long-term live imaging of embryos. This paper reports a spiral microfluidic device for effective sorting, trapping, and long-term live imaging of single C. elegans embryos under precisely controlled experimental conditions. The device successfully sorts embryos from a mixed population of C. elegans at different developmental stages via Dean vortices generated inside a spiral microchannel and traps the sorted embryos at single-cell resolution through hydrodynamic traps on the sidewall of the spiral channel for long-term imaging. Through the well-controlled microenvironment inside the microfluidic device, the response of the trapped C. elegans embryos to mechanical and chemical stimulation can be quantitatively measured. The experimental results show that a gentle hydrodynamic force would induce faster growth of embryos, and embryos developmentally arrested in the high-salinity solution could be rescued by the M9 buffer. The microfluidic device provides new avenues for easy, rapid, high-content screening of C. elegans embryos.

High-throughput submicron-resolution microscopy of Caenorhabditis elegans populations under strong immobilization by cooling cultivation plates

Despite its profound impact on biology, high-resolution in vivo microscopy largely remains low throughput because current immobilization techniques require substantial manual effort. We implement a simple cooling approach to immobilize entire populations of the nematode Caenorhabditis elegans directly on their cultivation plates. Counterintuitively, warmer temperatures immobilize animals much more effectively than the colder temperatures of prior studies and enable clear submicron-resolution fluorescence imaging, which is challenging under most immobilization techniques. We demonstrate 64× z-stack and time-lapse imaging of neurons in adults and embryos without motion blur. Compared to standard azide immobilization, cooling immobilization reduces the animal preparation and recovery time by >98%, significantly increasing experimental speed. High-throughput imaging of a fluorescent proxy in cooled animals and direct laser axotomy indicate that the transcription factor CREB underlies lesion conditioning. By obviating individual animal manipulation, our approach could empower automated imaging of large populations within standard experimental setups and workflows.

Massively parallel quantification of phenotypic heterogeneity in single-cell drug responses

Single-cell analysis tools have made substantial advances in characterizing genomic heterogeneity; however, tools for measuring phenotypic heterogeneity have lagged due to the increased difficulty of handling live biology. Here, we report a single-cell phenotyping tool capable of measuring image-based clonal properties at scales approaching 100,000 clones per experiment. These advances are achieved by exploiting a previously unidentified flow regime in ladder microfluidic networks that, under appropriate conditions, yield a mathematically perfect cell trap. Machine learning and computer vision tools are used to control the imaging hardware and analyze the cellular phenotypic parameters within these images. Using this platform, we quantified the responses of tens of thousands of single cell–derived acute myeloid leukemia (AML) clones to targeted therapy, identifying rare resistance and morphological phenotypes at frequencies down to 0.05%. This approach can be extended to higher-level cellular architectures such as cell pairs and organoids and on-chip live-cell fluorescence assays.

High-Temporal-Resolution smFISH Method for Gene Expression Studies in Caenorhabditis elegans Embryos

Recent development in fluorescence-based molecular tools has contributed significantly to developmental studies, including embryogenesis. Many of these tools rely on multiple steps of sample manipulation, so obtaining large sample sizes presents a major challenge as it can be labor-intensive and time-consuming. However, large sample sizes are required to uncover critical aspects of embryogenesis, for example, subtle phenotypic differences or gene expression dynamics. This problem is particularly relevant for single-molecule fluorescence in situ hybridization (smFISH) studies in Caenorhabditis elegans embryogenesis. Microfluidics can help address this issue by allowing a large number of samples and parallelization of experiments. However, performing efficient reagent exchange on chip for large numbers of embryos remains a bottleneck. Here, we present a microfluidic pipeline for large-scale smFISH imaging of C. elegans embryos with minimized labor. We designed embryo traps and engineered a protocol allowing for efficient chemical exchange for hundreds of C. elegans embryos simultaneously. Furthermore, the device design and small footprint optimize imaging throughput by facilitating spatial registration and enabling minimal user input. We conducted the smFISH protocol on chip and demonstrated that image quality is preserved. With one device replacing the equivalent of 10 glass slides of embryos mounted manually, our microfluidic approach greatly increases throughput. Finally, to highlight the capability of our platform to perform longitudinal studies with high temporal resolution, we conducted a temporal analysis of par-1 gene expression in early C. elegans embryos. The method demonstrated here paves the way for systematic high-temporal-resolution studies that will benefit large-scale RNAi and drug screens and in systems beyond C. elegans embryos.

Microfluidic approaches for Caenorhabditis elegans research

In the last decade, microfluidic methods have proven to be powerful tools for Caenorhabditis elegans research, offering advanced manipulation of worms and precise control of experimental conditions. The advantages of microfluidic chips include their capability of immobilization, automated sorting, and longitudinal measurement, and more. In this review, we focus on control components that are widely used in the design of microfluidic devices, and discuss their functions and working principles that enable advanced manipulation on a chip. Understanding these components will ease the onboarding of researchers inexperienced with microfluidics and help them bring the power of microfluidics to new applications.

An in vivo microfluidic study of bacterial transit in C. elegans nematodes

Caenorhabditis elegans (C. elegans) constitutes an important model organism for use in nutrition and aging studies. We report a novel method for studying the dynamics of Escherichia coli (E. coli) bacterial transit through the worms' intestine. A microfluidic chip was designed for alternating C. elegans on-chip culture and immobilization, thereby enabling periodic high-resolution time-lapse imaging at single-worm resolution over several days. Immobilization was achieved in a reversible way using arrays of tapered channels suitable for assay parallelization. Dedicated C. elegans feeding protocols were applied. Two E. coli bacterial strains, HT115 and OP50, respectively labeled with green fluorescent protein (GFP) and red fluorescent protein (RFP), were used as food source and imaged with fluorescence microscopy techniques to measure relevant parameters of the bacterial transit process. Feeding behavior and E. coli transit dynamics in the whole intestinal tract of the worms were characterized in an automated way over the first 3 days of adulthood, revealing both fast transit phenomena and variations in microbial accumulation. In particular, we studied the bacterial food transit periodicity in wild-type and eat-2 (ad465) mutant C. elegans strains in both trapped and free-swimming conditions. In order to further demonstrate the versatility of our microfluidic platform, we also studied drug-induced modifications of the bacterial transit by measuring the response of the worms' intestine to exposure to the neurotransmitter serotonin.

Automated phenotyping of Caenorhabditis elegans embryos with a high-throughput-screening microfluidic platform

The nematode Caenorhabditis elegans has been extensively used as a model multicellular organism to study the influence of osmotic stress conditions and the toxicity of chemical compounds on developmental and motility-associated phenotypes. However, the several-day culture of nematodes needed for such studies has caused researchers to explore alternatives. In particular, C. elegans embryos, due to their shorter developmental time and immobile nature, could be exploited for this purpose, although usually their harvesting and handling is tedious. Here, we present a multiplexed, high-throughput and automated embryo phenotyping microfluidic approach to observe C. elegans embryogenesis after the application of different chemical compounds. After performing experiments with up to 800 embryos per chip and up to 12 h of time-lapsed imaging per embryo, the individual phenotypic developmental data were collected and analyzed through machine learning and image processing approaches. Our proof-of-concept platform indicates developmental lag and the induction of mitochondrial stress in embryos exposed to high doses (200 mM) of glucose and NaCl, while small doses of sucrose and glucose were shown to accelerate development. Overall, our new technique has potential for use in large-scale developmental biology studies and opens new avenues for very rapid high-throughput and high-content screening using C. elegans embryos.

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.

Understanding the Mechanobiology of Early Mammalian Development through Bioengineered Models

Research in developmental biology has been recently enriched by a multitude of in vitro models recapitulating key milestones of mammalian embryogenesis. These models obviate the challenge posed by the inaccessibility of implanted embryos, multiply experimental opportunities, and favor approaches traditionally associated with organoids and tissue engineering. Here, we provide a perspective on how these models can be applied to study the mechano-geometrical contributions to early mammalian development, which still escape direct verification in species that develop in utero. We thus outline new avenues for robust and scalable perturbation of geometry and mechanics in ways traditionally limited to non-implanting developmental models.

Microfluidics as an Emerging Precision Tool in Developmental Biology

Microfluidics has become a precision tool in modern biology. It enables omics data to be obtained from individual cells, as compared to averaged signals from cell populations, and it allows manipulation of biological specimens in entirely new ways. Cells and organisms can be perturbed at extraordinary spatiotemporal resolution, revealing mechanistic insights that would otherwise remain hidden. In this perspective article, we discuss the current and future impact of microfluidic technology in the field of developmental biology. In addition, we provide detailed information on how to start using this technology even without prior experience.

On-chip technology for single-cell arraying, electrorotation-based analysis and selective release

This paper reports a method for label-free single-cell biophysical analysis of multiple cells trapped in suspension by electrokinetic forces. Tri-dimensional pillar electrodes arranged along the width of a microfluidic chamber define actuators for single cell trapping and selective release by electrokinetic force. Moreover, a rotation can be induced on the cell in combination with a negative DEP force to retain the cell against the flow. The measurement of the rotation speed of the cell as a function of the electric field frequency define an electrorotation spectrum that allows to study the dielectric properties of the cell. The system presented here shows for the first time the simultaneous electrorotation analysis of multiple single cells in separate micro cages that can be selectively addressed to trap and/or release the cells. Chips with 39 micro-actuators of different interelectrode distance were fabricated to study cells with different sizes. The extracted dielectric properties of Henrietta Lacks, human embryonic kidney 293, and human immortalized T lymphocytes cells were found in agreements with previous findings. Moreover, the membrane capacitance of M17 neuroblastoma cells was investigated and found to fall in in the range of 7.49 ± 0.39 mF/m2 .

Microfluidics for mechanobiology of model organisms

Mechanical stimuli play a critical role in organ development, tissue homeostasis, and disease. Understanding how mechanical signals are processed in multicellular model systems is critical for connecting cellular processes to tissue- and organism-level responses. However, progress in the field that studies these phenomena, mechanobiology, has been limited by lack of appropriate experimental techniques for applying repeatable mechanical stimuli to intact organs and model organisms. Microfluidic platforms, a subgroup of microsystems that use liquid flow for manipulation of objects, are a promising tool for studying mechanobiology of small model organisms due to their size scale and ease of customization. In this work, we describe design considerations involved in developing a microfluidic device for studying mechanobiology. Then, focusing on worms, fruit flies, and zebrafish, we review current microfluidic platforms for mechanobiology of multicellular model organisms and their tissues and highlight research opportunities in this developing field.

High-throughput live-imaging of embryos in microwell arrays using a modular specimen mounting system

High-throughput live-imaging of embryos is an essential technique in developmental biology, but it is difficult and costly to mount and image embryos in consistent conditions. Here, we present OMMAwell, a simple, reusable device to easily mount dozens of embryos in arrays of agarose microwells with customizable dimensions and spacing. OMMAwell can be configured to mount specimens for upright or inverted microscopes, and includes a reservoir to hold live-imaging medium to maintain constant moisture and osmolarity of specimens during time-lapse imaging. All device components can be fabricated by cutting pieces from a sheet of acrylic using a laser cutter or by making them with a 3D printer. We demonstrate how to design a custom mold and use it to live-image dozens of embryos at a time. We include descriptions, schematics, and design files for 13 additional molds for nine animal species, including most major traditional laboratory models and a number of emerging model systems. Finally, we provide instructions for researchers to customize OMMAwell inserts for embryos or tissues not described herein.

3D Hybrid Small Scale Devices

Interfacing nano/microscale elements with biological components in 3D contexts opens new possibilities for mimicry, bionics, and augmentation of organismically and anatomically inspired materials. Abiotic nanoscale elements such as plasmonic nanostructures, piezoelectric ribbons, and thin film semiconductor devices interact with electromagnetic fields to facilitate advanced capabilities such as communication at a distance, digital feedback loops, logic, and memory. Biological components such as proteins, polynucleotides, cells, and organs feature complex chemical synthetic networks that can regulate growth, change shape, adapt, and regenerate. Abiotic and biotic components can be integrated in all three dimensions in a well-ordered and programmed manner with high tunability, versatility, and resolution to produce radically new materials and hybrid devices such as sensor fabrics, anatomically mimetic microfluidic modules, artificial tissues, smart prostheses, and bionic devices. In this critical Review, applications of small scale devices in 3D hybrid integration, biomicrofluidics, advanced prostheses, and bionic organs are discussed.

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.

Microfluidics-enabled phenotyping of a whole population of C. elegans worms over their embryonic and post-embryonic development at single-organism resolution

The organism Caenorhabditis elegans is a performant model system for studying human biological processes and diseases, but until now all phenome data are produced as population-averaged read-outs. Monitoring of individual responses to drug treatments would however be more informative. Here, a new strategy to track different phenotypic traits of individual C. elegans nematodes throughout their full life-cycle-i.e., embryonic and post-embryonic development, until adulthood onset, differently from life-span-is presented. In an automated fashion, single worms were synchronized, isolated, and cultured from egg to adulthood in a microfluidic device, where their identity was preserved during their whole development. Several phenotypes were monitored and quantified for each animal, resulting in high-content phenome data. Specifically, the method was validated by analyzing the response of C. elegans to doxycycline, an antibiotic fairly well-known to prolong the development and activate mitochondrial stress-response pathways in different species. Interestingly, the obtained extensive single-worm phenome not only confirmed the dramatic doxycycline effect on the worm developmental delay, but more importantly revealed subtle yet severe treatment-dependent phenotypes that are representative of minority subgroups and would have otherwise stayed hidden in an averaged dataset. Such heterogeneous response started during the embryonic development, which makes essential having a dedicated chip that allows including this early developmental stage in the drug assay. Our approach would therefore allow elucidating pharmaceutical or therapeutic responses that so far were still being overlooked.

Integrated Microfluidic Device for Drug Studies of Early C. Elegans Embryogenesis

Small molecules inhibitors are powerful tools for studying multiple aspects of cell biology and stand at the forefront of drug discovery pipelines. However, in the early Caenorhabditis elegans (C. elegans) embryo, which is a powerful model system for cell and developmental biology, the use of small molecule inhibitors has been limited by the impermeability of the embryonic eggshell, the low-throughput manual embryo isolation methods, and the lack of well-controlled drug delivery protocols. This work reports a fully integrated microfluidic approach for studies of C. elegans early embryogenesis, including the possibility of testing small molecule inhibitors with increased throughput and versatility. The setup enables robust on-chip extraction of embryos from gravid adult worms in a dedicated pillar array chamber by mechanical compression, followed by rapid fluidic transfer of embryos into an adjacent microtrap array. Parallel analysis of ≈100 embryos by high-resolution time-lapse imaging from the one-cell stage zygote until hatching can be performed with this device. The implementation of versatile microfluidic protocols, in particular time-controlled and reversible drug delivery to on-chip immobilized embryos, demonstrates the potential of the device for biochemical and pharmacological assays.

A design of experiment approach for efficient multi-parametric drug testing using a Caenorhabditis elegans model

When studying the drug effectiveness towards a target model, one should distinguish the effects of the drug itself and of all the other factors that could influence the screening outcome. This comprehensive knowledge is crucial, especially when model organisms are used to study the drug effect at a systemic level, as a higher number of factors can influence the drug-testing outcome. Covering the entire experimental domain and studying the effect of the simultaneous change in several factors would require numerous experiments, which are costly and time-consuming. Therefore, a design of experiment (DoE) approach in drug-testing is emerging as a robust and efficient method to reduce the use of resources, while maximizing the knowledge of the process. Here, we used a 3-factor-Doehlert DoE to characterize the concentration-dependent effect of the drug doxycycline on the development duration of the nematode Caenorhabditis elegans. To cover the experimental space, 13 experiments were designed and performed, where different doxycycline concentrations were tested, while also varying the temperature and the food amount, which are known to influence the duration of C. elegans development. A microfluidic platform was designed to isolate and culture C. elegans larvae, while testing the doxycycline effect with full control of temperature and feeding over the entire development. Our approach allowed predicting the doxycycline effect on C. elegans development in the complete drug concentration/temperature/feeding experimental space, maximizing the understanding of the effect of this antibiotic on the C. elegans development and paving the way towards a standardized and optimized drug-testing process.

Flexible and disposable paper- and plastic-based gel micropads for nematode handling, imaging, and chemical testing

Today, the area of point-of-care diagnostics is synonymous with paper microfluidics where cheap, disposable, and on-the-spot detection toolkits are being developed for a variety of chemical tests. In this work, we present a novel application of microfluidic paper-based analytical devices (μPADs) to study the behavior of a small model nematode, Caenorhabditis elegans. We describe schemes of μPAD fabrication on paper and plastic substrates where membranes are created in agarose and Pluronic gel. Methods are demonstrated for loading, visualizing, and transferring single and multiple nematodes. Using an anthelmintic drug, levamisole, we show that chemical testing on C. elegans is easily performed because of the open device structure. A custom program is written to automatically recognize individual worms on the μPADs and extract locomotion parameters in real-time. The combination of μPADs and the nematode tracking program provides a relatively low-cost, simple-to-fabricate imaging and screening assay (compared to standard agarose plates or polymeric microfluidic devices) for non-microfluidic, nematode laboratories.

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.

Forward and reverse genetics approaches to uncover metabolic aging pathways in Caenorhabditis elegans

The biological mechanisms of aging have been studied in depth and prominent findings in this field promote the development of new therapies for age-associated disorders. Various model organisms are used for research on aging; among these, the nematode Caenorhabditis elegans has been widely used and has provided valuable knowledge in determining the regulatory mechanisms driving the aging process. Many genes involved in lifespan regulation are associated with metabolic pathways and are influenced by genetic and environmental factors. In line with this, C. elegans provides a promising platform to study such gene by environment interactions, in either a reverse or forward genetics approach. In this review, we discuss longevity mechanisms related to metabolic networks that have been discovered in C. elegans. We also highlight the use of wild populations to study the complex genetic basis of natural variation for quantitative traits that mediate longevity.

Choosing proper fluorescent dyes, proteins, and imaging techniques to study mitochondrial dynamics in mammalian cells

Mitochondrial dynamics refers to the processes maintaining mitochondrial homeostasis, including mitochondrial fission, fusion, transport, biogenesis, and mitophagy. Mitochondrial dynamics is essential for maintaining the metabolic function of mitochondria as well as their regulatory roles in cell signaling. In this review, we summarize the recently developed imaging techniques for studying mitochondrial dynamics including: mitochondrial-targeted fluorescent proteins and dyes, live-cell imaging using photoactivation, photoswitching and cell fusion, mitochondrial transcription and replication imaging by in situ hybridization, and imaging mitochondrial dynamics by super-resolution microscopy. Moreover, we discuss examples of how to choose and combine proper fluorescent dyes and/or proteins.

All-in-one 3D printed microscopy chamber for multidimensional imaging, the UniverSlide

While live 3D high resolution microscopy techniques are developing rapidly, their use for biological applications is partially hampered by practical difficulties such as the lack of a versatile sample chamber. Here, we propose the design of a multi-usage observation chamber adapted for live 3D bio-imaging. We show the usefulness and practicality of this chamber, which we named the UniverSlide, for live imaging of two case examples, namely multicellular systems encapsulated in sub-millimeter hydrogel shells and zebrafish larvae. We also demonstrate its versatility and compatibility with all microscopy devices by using upright or inverted microscope configurations after loading the UniverSlide with fixed or living samples. Further, the device is applicable for medium/high throughput screening and automatized multi-position image acquisition, providing a constraint-free but stable and parallelized immobilization of the samples. The frame of the UniverSlide is fabricated using a stereolithography 3D printer, has the size of a microscopy slide, is autoclavable and sealed with a removable lid, which makes it suitable for use in a controlled culture environment. We describe in details how to build this chamber and we provide all the files necessary to print the different pieces in the lab.

A multiscale study of the role of dynamin in the regulation of glucose uptake

Cells- and organisms-on-a-chip strategies were used to highlight the role of the molecular motor dynamin in regulating the translocation of specific glucose transporters.

On-chip microfluidic biocommunication assay for studying male-induced demise in C. elegans hermaphrodites

Like other animals, C. elegans nematodes have the ability to socially interact and to communicate through exchange and sensing of small soluble signaling compounds that help them cope with complex environmental conditions. For the time being, worm biocommunication assays are being performed mainly on agar plates; however, microfluidic assays may provide significant advantages compared to traditional methods, such as control of signaling molecule concentrations and gradients or confinement of distinct worm populations in different microcompartments. Here, we propose a microfluidic device for studying signaling via diffusive secreted compounds between two specific C. elegans populations over prolonged durations. In particular, we designed a microfluidic assay to investigate the biological process of male-induced demise, i.e. lifespan shortening and accelerated age-related phenotype alterations, in C. elegans hermaphrodites in the presence of a physically separated male population. For this purpose, male and hermaphrodite worm populations were confined in adjacent microchambers on the chip, whereas molecules secreted by males could be exchanged between both populations by periodically activating the controlled fluidic transfer of μl-volume aliquots of male-conditioned medium. For male-conditioned hermaphrodites, we observed a reduction of 4 days in mean lifespan compared to the non-conditioned on-chip culture. We also observed an enhanced muscle decline, as expressed by a faster decrease in the thrashing frequency and the appearance of vacuolar-like structures indicative of accelerated aging. The chip was placed in an incubator at 20 °C for accurate control of the lifespan assay conditions. An on-demand bacteria feeding protocol was applied, and the worms were observed during long-term on-chip culture over the whole worm lifespan.

The Movement Tracker: A Flexible System for Automated Movement Analysis in Invertebrate Model Organisms

Phenotyping strategies in simple model organisms such as D. melanogaster and C. elegans are often broadly limited to growth, aging, and fitness. Recently, a number of physical setups and video tracking software suites have been developed to allow for accurate, quantitative, and high-throughput analysis of movement in flies and worms. However, many of these systems require precise experimental setups and/or fixed recording formats. We report here an update to the Parallel Worm Tracker software, which we termed the Movement Tracker. The Movement Tracker allows variable experimental setups to provide cross-platform automated processing of a variety of movement characteristics in both worms and flies and permits the use of simple physical setups that can be readily implemented in any laboratory. This software allows high-throughput processing capabilities and high levels of flexibility in video analysis, providing quantitative movement data on C. elegans and D. melanogaster in a variety of different conditions. © 2016 by John Wiley & Sons, Inc.

Acoustofluidic Rotational Manipulation of Cells and Organisms Using Oscillating Solid Structures

A polydimethylsiloxane microchannel featuring sidewall sharp-edge structures and bare channels, and a piezoelement transducer is attached to a thin glass slide. When an external acoustic field is applied to the microchannel, the oscillation of the sharp-edge structures and the thin glass slide generate acoustic streaming flows which in turn rotate single cells and C. elegans in-plane and out-of-plane.

Microfluidic Devices in Advanced Caenorhabditis elegans Research

The study of model organisms is very important in view of their potential for application to human therapeutic uses. One such model organism is the nematode worm, Caenorhabditis elegans. As a nematode, C. elegans have ~65% similarity with human disease genes and, therefore, studies on C. elegans can be translated to human, as well as, C. elegans can be used in the study of different types of parasitic worms that infect other living organisms. In the past decade, many efforts have been undertaken to establish interdisciplinary research collaborations between biologists, physicists and engineers in order to develop microfluidic devices to study the biology of C. elegans. Microfluidic devices with the power to manipulate and detect bio-samples, regents or biomolecules in micro-scale environments can well fulfill the requirement to handle worms under proper laboratory conditions, thereby significantly increasing research productivity and knowledge. The recent development of different kinds of microfluidic devices with ultra-high throughput platforms has enabled researchers to carry out worm population studies. Microfluidic devices primarily comprises of chambers, channels and valves, wherein worms can be cultured, immobilized, imaged, etc. Microfluidic devices have been adapted to study various worm behaviors, including that deepen our understanding of neuromuscular connectivity and functions. This review will provide a clear account of the vital involvement of microfluidic devices in worm biology.

Microfluidic Approaches for Manipulating, Imaging, and Screening C. elegans

The nematode C. elegans (worm) is a small invertebrate animal widely used in studies related to fundamental biological processes, disease modelling, and drug discovery. Due to their small size and transparent body, these worms are highly suitable for experimental manipulations. In recent years several microfluidic devices and platforms have been developed to accelerate worm handling, phenotypic studies and screens. Here we review major tools and briefly discuss their usage in C. elegans research.

Microfluidics for High-Throughput Quantitative Studies of Early Development

Developmental biology has traditionally relied on qualitative analyses; recently, however, as in other fields of biology, researchers have become increasingly interested in acquiring quantitative knowledge about embryogenesis. Advances in fluorescence microscopy are enabling high-content imaging in live specimens. At the same time, microfluidics and automation technologies are increasing experimental throughput for studies of multicellular models of development. Furthermore, computer vision methods for processing and analyzing bioimage data are now leading the way toward quantitative biology. Here, we review advances in the areas of fluorescence microscopy, microfluidics, and data analysis that are instrumental to performing high-content, high-throughput studies in biology and specifically in development. We discuss a case study of how these techniques have allowed quantitative analysis and modeling of pattern formation in the Drosophila embryo.

Versatile size-dependent sorting of C. elegans nematodes and embryos using a tunable microfluidic filter structure

The roundworm Caenorhabditis elegans (C. elegans) is a powerful model organism for addressing fundamental biological questions related to human disease and aging. Its life cycle consists of an embryo stage, four larval stages that can be clearly distinguished by size and different morphological features, and adulthood. Many worm-based bio-assays require stage- or age-synchronized worm populations, for example for studying the life cycle and aging of worms under different pharmacological conditions or to avoid misinterpretation of results due to overlap of stage-specific response in general. Here, we present a new microfluidic approach for size-dependent sorting of C. elegans nematodes on-chip. We take advantage of the external pressure-deformable profile of polydimethylsiloxane (PDMS) transfer channels that connect two on-chip worm chambers. The pressure-controlled effective cross-section of these channels creates adjustable filter structures that can be easily tuned for a specific worm sorting experiment, without changing the design parameters of the device itself. By optimizing the control pressure settings, we can extract larvae of a specific development stage from a mixed worm culture with an efficiency close to 100% and with a throughput of up to 3.5 worms per second. Our approach also allows us to generate mixed populations of larvae of adjacent stages or to adjust their ratio directly in the microfluidic chamber. Moreover, using the same device, we demonstrated extraction of embryos from adult worm populations for subsequent culture of accurately age-synchronized nematode populations or embryo-based assays. Considering that our sorting device is merely based on geometrical parameters and operated by simple fluidic and pressure control, we believe that it has strong potential for use in advanced, automated, microfluidic C. elegans-based assay platforms.

Active bioparticle manipulation in microfluidic systems

The motion of bioparticles in a microfluidic environment can be actively controlled using several tuneable mechanisms, including hydrodynamic, electrophoresis, dielectrophoresis, magnetophoresis, acoustophoresis, thermophoresis and optical forces.