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

Difference in Intestine Content of Caenorhabditis elegans When Fed on Non-Pathogenic or Pathogenic Bacteria

We investigated the bacterial food digestion and accumulation in wild-type adult Caenorhabditis elegans (C. elegans) worms that have fed on either non-pathogenic RFP-expressing Escherichia coli (E. coli) OP50 or pathogenic-RFP-expressing Pseudomonas aeruginosa (P. aeruginosa) PAO1 during the first 4 days of adulthood. Once the worms had completed their planned feeding cycles, they were loaded on microfluidic chips, where they were fixed to allow high-resolution z-stack fluorescence imaging of their intestines utilizing a Spinning Disk Confocal Microscope (SDCM) equipped with a high-resolution oil-immersion objective (60×). IMARIS software was used to visualize and analyze the obtained images, resulting in the production of three-dimensional constructs of the intestinal bacterial load. We discovered two distinct patterns for the bacteria-derived fluorescence signal in the intestine: (i) individual fluorescent spots, originating from intact bacteria, were present in the fluorescent E. coli-OP50-fed worms, and (ii) individual fluorescent spots (originating from intact bacteria) were dispersed in large regions of diffuse fluorescence (RDF), originating from disrupted bacteria, in fluorescent P. aeruginosa-PAO1-fed worms. We performed a semi-automated single-worm-resolution quantitative analysis of the intestinal bacterial load, which showed that the intestinal bacterial load generally increases with age of the worms, but more rapidly for the fluorescent P. aeruginosa-PAO1-fed worms.

High-resolution imaging and analysis of the intestinal bacterial load of Caenorhabditis elegans during early adulthood

We study the presence within the worm Caenorhabditis elegans (C. elegans) of a fluorescent strain of the worm's bacterial food (Escherichia coli (E. coli) OP50) during early adulthood. Use of a microfluidic chip based on a thin glass coverslip substrate allows investigation of the intestinal bacterial load using a Spinning Disk Confocal Microscope (SDCM) equipped with a high-resolution objective (60×). High-resolution z-stack fluorescence images of the gut bacteria in adult worms, which were loaded in the microfluidic chip and subsequently fixed, were analyzed using IMARIS software and 3D reconstructions of the intestinal bacterial load in the worms were obtained. We present an automated bivariate histogram analysis of the volumes and intensities of the bacterial spots for each worm and find that, as the worms age, the bacterial load in their hindguts increases. We show the advantage of single-worm resolution automated analysis for bacterial load studies and anticipate that the methods described in our work can be easily implemented in existing microfluidic solutions to enable thorough studies of bacterial proliferation.

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.

Tetracycline-induced mitohormesis mediates disease tolerance against influenza

Mitohormesis defines the increase in fitness mediated by adaptive responses to mild mitochondrial stress. Tetracyclines inhibit not only bacterial but also mitochondrial translation, thus imposing a low level of mitochondrial stress on eukaryotic cells. We demonstrate in cell and germ-free mouse models that tetracyclines induce a mild adaptive mitochondrial stress response (MSR), involving both the ATF4-mediated integrative stress response and type I interferon (IFN) signaling. To overcome the interferences of tetracyclines with the host microbiome, we identify tetracycline derivatives that have minimal antimicrobial activity, yet retain full capacity to induce the MSR, such as the lead compound, 9-tert-butyl doxycycline (9-TB). The MSR induced by doxycycline (Dox) and 9-TB improves survival and disease tolerance against lethal influenza virus (IFV) infection when given preventively. 9-TB, unlike Dox, did not affect the gut microbiome and also showed encouraging results against IFV when given in a therapeutic setting. Tolerance to IFV infection is associated with the induction of genes involved in lung epithelial cell and cilia function, and with downregulation of inflammatory and immune gene sets in lungs, liver, and kidneys. Mitohormesis induced by non-antimicrobial tetracyclines and the ensuing IFN response may dampen excessive inflammation and tissue damage during viral infections, opening innovative therapeutic avenues.

An In Vivo Microfluidic Study of Bacterial Load Dynamics and Absorption in the C. elegans Intestine

Caenorhabditiselegans (C. elegans) has gained importance as a model for studying host-microbiota interactions and bacterial infections related to human pathogens. Assessing the fate of ingested bacteria in the worm's intestine is therefore of great interest, in particular with respect to normal bacterial digestion or intestinal colonization by pathogens. Here, we report an in vivo study of bacteria in the gut of C. elegans. We take advantage of a polydimethylsiloxane (PDMS) microfluidic device enabling passive immobilization of adult worms under physiological conditions. Non-pathogenic Escherichia coli (E. coli) bacteria expressing either pH-sensitive or pH-insensitive fluorescence reporters as well as fluorescently marked indigestible microbeads were used for the different assays. Dynamic fluorescence patterns of the bacterial load in the worm gut were conveniently monitored by time-lapse imaging. Cyclic motion of the bacterial load due to peristaltic activity of the gut was observed and biochemical digestion of E. coli was characterized by high-resolution fluorescence imaging of the worm's intestine. We could discriminate between individual intact bacteria and diffuse signals related to disrupted bacteria that can be digested. From the decay of the diffuse fluorescent signal, we determined a digestion time constant of 14 ± 4 s. In order to evaluate the possibility to perform infection assays with our platform, immobilized C. elegans worms were fed pathogenic Mycobacterium marinum (M. marinum) bacteria. We analyzed bacterial fate and accumulation in the gut of N2 worms and mitochondrial stress response in a hsp-6::gfp mutant.

A polymer index-matched to water enables diverse applications in fluorescence microscopy

We demonstrate diffraction-limited and super-resolution imaging through thick layers (tens-hundreds of microns) of BIO-133, a biocompatible, UV-curable, commercially available polymer with a refractive index (RI) matched to water. We show that cells can be directly grown on BIO-133 substrates without the need for surface passivation and use this capability to perform extended time-lapse volumetric imaging of cellular dynamics 1) at isotropic resolution using dual-view light-sheet microscopy, and 2) at super-resolution using instant structured illumination microscopy. BIO-133 also enables immobilization of 1) Drosophila tissue, allowing us to track membrane puncta in pioneer neurons, and 2) Caenorhabditis elegans, which allows us to image and inspect fine neural structure and to track pan-neuronal calcium activity over hundreds of volumes. Finally, BIO-133 is compatible with other microfluidic materials, enabling optical and chemical perturbation of immobilized samples, as we demonstrate by performing drug and optogenetic stimulation on cells and C. elegans.

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.

PDMS filter structures for size-dependent larval sorting and on-chip egg extraction of C. elegans

C. elegans-based assays require age-synchronized populations prior to experimentation to achieve standardized sets of worm populations, due to which age-induced heterogeneous phenotyping effects can be avoided. There have been several approaches to synchronize populations of C. elegans at certain larval stages; however, many of these methods are tedious, complex and have low throughput. In this work, we demonstrate a polydimethylsiloxane (PDMS) microfluidic filtering device for high-throughput, efficient, and extremely rapid sorting of mixed larval populations of C. elegans. Our device consists of three plasma-activated and bonded PDMS parts and permits sorting of mixed populations of two consecutive larval stages in a matter of minutes. After sorting, we also retain the remaining larval stage of the initially mixed worm population on the chip, thereby enabling collection of the two sorted larval populations from the device. We demonstrated that the target larvae could be collected from a mixed worm population by cascading these devices. Our approach is based on only passive hydrodynamics filter structures, resulting in a user-friendly and reusable tool. In addition, we employed the equivalent of a standard bleaching procedure that is practiced in standard worm culture on agar plates for embryo harvesting on our chip, and we demonstrated rapid egg extraction and subsequent harvesting of a synchronized L1 larvae population.

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.

Automation of C. elegans lifespan measurement

Aging is a fundamental biological process that is still not fully understood. As many of the most significant human diseases have aging as their greatest risk factor, a better understanding of aging potentially has enormous practical implications in treating these diseases. The nematode C. elegans is an exceptionally useful genetic model organism that had been used with great success to shed light on many genes and pathways that are involved in aging. Many of these pathways and mechanisms have been shown to be conserved through mammals. The standard methods for assaying survival in C. elegans to measure changes in lifespan are tedious and time consuming. This limits the throughput and productivity of C. elegans aging researchers. In recent years, many inroads have been made into automating various facets of the collection and analysis of C. elegans lifespan experimental data. The advances described in this review all work to ameliorate some of the hurdles that come with manual worm lifespan scoring, by automating or eliminating some of the most time consuming aspects of the assay. By greatly increasing the throughput of lifespan assays, these methods will enable types of experiments (e.g., drug library screens) whose scale is currently impractical. These methods have already proved exceptionally useful, and some of them are likely to be the predecessors of even more refined methods that could lead to breakthroughs in the ability to study lifespan in C. elegans. This could in turn potentially revolutionize our understanding of the basic biology of aging, and one day lead to treatments that could offset or delay age-related diseases in humans.

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.