More Like this

1. Caenorhabditis elegans processes sensory information to choose between freeloading and self-defense strategies

   https://doi.org/10.7554/eLife.56186  

   Schiffer, Jodie A ; Servello, Francesco A ; Heath, William R ; Amrit, Francis Raj ; Stumbur, Stephanie V ; Eder, Matthias ; Martin, Olivier MF ; Johnsen, Sean B ; Stanley, Julian A ; Tam, Hannah ; et al ( May 2020 , eLife)

   null (Ed.)

   Cells of all kinds often wage chemical warfare against each other. Hydrogen peroxide is often the weapon of choice on the microscopic battlefield, where it is used to incapacitate opponents or to defend against attackers. For example, some plants produce hydrogen peroxide in response to infection to fight off disease-causing microbes. Individual cells have also evolved defenses to prevent or repair ‘injuries’ caused by hydrogen peroxide. These are similar across many different species. They include enzymes called catalases, which break down hydrogen peroxide, and others to repair damage. However, scientists still do not fully understand how animals and other multicellular organisms might coordinate these defenses across their cells. Caenorhabditis elegans is a microscopic species of worm that lives in rotting fruits. It often encounters the threat of cellular warfare: many types of bacteria in its environment generate hydrogen peroxide, and some can make enough to kill the worms outright. Like other organisms, C. elegans also produces catalases to defend itself against hydrogen peroxide attacks. However, it must activate its defenses at the right time; if it did so when they were not needed, this would result in a detrimental energy ‘cost’ to the worm. Although C. elegans is a small organism containing only a defined number of cells, exactly why and how it switches its chemical defenses on or off remains unknown. Schiffer et al. therefore set out to determine how C. elegans controls these defenses, focusing on the role of the brain in detecting and processing information from its environment. Experiments looking at the brains of genetically manipulated worms revealed a circuit of sensory nerve cells whose job is to tell the rest of the worm’s tissues that they no longer need to produce defense enzymes. Crucially, the circuit became active when the worms sensed E. coli bacteria nearby. Bacteria in the same family as E. coli are normally found in in the same habitat as C. elegans and these bacteria are also known to make enzymes of their own to eliminate hydrogen peroxide around them. These results indicate that C. elegans can effectively decide, based on the activity of its circuit, when to use its own defenses and when to ‘freeload’ off those of neighboring bacteria. This work is an important step towards understanding how sensory circuits in the brain can control hydrogen peroxide defenses in multicellular organisms. In the future, it could help researchers work out how more complex animals, like humans, coordinate their cellular defenses, and therefore potentially yield new strategies for improving health and longevity. 

   more » « less
2. Selection of food patches by sympatric herbivores in response to concealment and distance from a refuge

   https://doi.org/10.1002/ece3.1940  

   Crowell, Miranda M. ; Shipley, Lisa A. ; Camp, Meghan J. ; Rachlow, Janet L. ; Forbey, Jennifer S. ; Johnson, Timothy R. ( March 2016 , Ecology and Evolution)

   Small herbivores face risks of predation while foraging and are often forced to trade off food quality for safety. Life history, behaviour, and habitat of predator and prey can influence these trade‐offs. We compared how two sympatric rabbits (pygmy rabbit,Brachylagus idahoensis; mountain cottontail,Sylvilagus nuttallii) that differ in size, use of burrows, and habitat specialization in the sagebrush‐steppe of westernNorthAmerica respond to amount and orientation of concealment cover and proximity to burrow refuges when selecting food patches. We predicted that both rabbit species would prefer food patches that offered greater concealment and food patches that were closer to burrow refuges. However, because pygmy rabbits are small, obligate burrowers that are restricted to sagebrush habitats, we predicted that they would show stronger preferences for greater cover, orientation of concealment, and patches closer to burrow refuges. We offered two food patches to individuals of each species during three experiments that either varied in the amount of concealment cover, orientation of concealment cover, or distance from a burrow refuge. Both species preferred food patches that offered greater concealment, but pygmy rabbits generally preferred terrestrial and mountain cottontails preferred aerial concealment. Only pygmy rabbits preferred food patches closer to their burrow refuge. Different responses to concealment and proximity to burrow refuges by the two species likely reflect differences in perceived predation risks. Because terrestrial predators are able to dig for prey in burrows, animals like pygmy rabbits that rely on burrow refuges might select food patches based more on terrestrial concealment. In contrast, larger habitat generalists that do not rely on burrow refuges, like mountain cottontails, might trade off terrestrial concealment for visibility to detect approaching terrestrial predators. This study suggests that body size and evolutionary adaptations for using habitat, even in closely related species, might influence anti‐predator behaviors in prey species.

    

   more » « less
3. CUT&RUN for Chromatin Profiling in Caenorhabditis elegans

   https://doi.org/10.1002/cpz1.445  

   Emerson, Felicity J. ; Lee, Siu Sylvia ( June 2022 , Current Protocols)

   Cleavage under targets and release using nuclease (CUT&RUN) is a recently developed chromatin profiling technique that uses a targeted micrococcal nuclease cleavage strategy to obtain high‐resolution binding profiles of protein factors or to map histones with specific post‐translational modifications. Due to its high sensitivity, CUT&RUN allows quality binding profiles to be obtained with only a fraction of the starting material and sequencing depth typically required for other chromatin profiling techniques such as chromatin immunoprecipitation. Although CUT&RUN has been widely adopted in multiple model systems, it has rarely been utilized inCaenorhabditis elegans, a model system of great importance to genomic research. Cell dissociation techniques, which are required for this approach, can be challenging inC. elegansdue to the toughness of the worm's cuticle and the sensitivity of the cells themselves. Here, we describe a robust CUT&RUN protocol for use inC. elegansto determine the genome‐wide localization of protein factors and specific histone marks. With a simple protocol utilizing live, uncrosslinked tissue as the starting material, performing CUT&RUN in worms has the potential to produce physiologically relevant data at a higher resolution than chromatin immunoprecipitation. This protocol involves a simple dissociation step to uniformly permeabilize worms while avoiding sample loss or cell damage, resulting in high‐quality CUT&RUN profiles with as few as 100 worms and detectable signal with as few as 10 worms. This represents a significant advancement over chromatin immunoprecipitation, which typically uses thousands or hundreds of thousands of worms for a single experiment. The protocols presented here provide a detailed description of worm growth, sample preparation, CUT&RUN workflow, library preparation for high‐throughput sequencing, and a basic overview of data analysis, making CUT&RUN simple and accessible for any worm lab. © 2022 Wiley Periodicals LLC.

   Basic Protocol 1: Growth and synchronization ofC. elegans

   Basic Protocol 2: Worm dissociation, sample preparation, and optimization

   Basic Protocol 3: CUT&RUN chromatin profiling

   Alternate Protocol: Improving CUT&RUN signal using a secondary antibody

   Basic Protocol 4: CUT&RUN library preparation for Illumina high‐throughput sequencing

   Basic Protocol 5: Basic data analysis using Linux

    

   more » « less
4. Patterns of Genomic Diversity in a Fig-Associated Close Relative of Caenorhabditis elegans

   https://doi.org/10.1093/gbe/evae020  

   Woodruff, Gavin C ; Willis, John H ; Phillips, Patrick C ( February 2024 , Genome Biology and Evolution)

   Baer, Charles (Ed.)

   The evolution of reproductive mode is expected to have profound impacts on the genetic composition of populations. At the same time, ecological interactions can generate close associations among species, which can in turn generate a high degree of overlap in their spatial distributions. Caenorhabditis elegans is a hermaphroditic nematode that has enabled extensive advances in developmental genetics. Caenorhabditis inopinata, the sister species of C. elegans, is a gonochoristic nematode that thrives in figs and obligately disperses on fig wasps. Here, we describe patterns of genomic diversity in C. inopinata. We performed RAD-seq on individual worms isolated from the field across three Okinawan island populations. C. inopinata is about five times more diverse than C. elegans. Additionally, C. inopinata harbors greater differences in diversity among functional genomic regions (such as between genic and intergenic sequences) than C. elegans. Conversely, C. elegans harbors greater differences in diversity between high-recombining chromosome arms and low-recombining chromosome centers than C. inopinata. FST is low among island population pairs, and clear population structure could not be easily detected among islands, suggesting frequent migration of wasps between islands. These patterns of population differentiation appear comparable with those previously reported in its fig wasp vector. These results confirm many theoretical population genetic predictions regarding the evolution of reproductive mode and suggest C. inopinata population dynamics may be driven by wasp dispersal. This work sets the stage for future evolutionary genomic studies aimed at understanding the evolution of sex as well as the evolution of ecological interactions.

    

   more » « less
5. Biosynthetic tailoring of existing ascaroside pheromones alters their biological function in C. elegans

   https://doi.org/10.7554/eLife.33286  

   Zhou, Yue ; Wang, Yuting ; Zhang, Xinxing ; Bhar, Subhradeep ; Jones Lipinski, Rachel A ; Han, Jungsoo ; Feng, Likui ; Butcher, Rebecca A ( June 2018 , eLife)

   Small roundworms such as Caenorhabditis elegans release chemical signals called ascarosides in order to communicate with other worms of the same species. Using the ascarosides, the worm can tell its friends, for example, how crowded the neighborhood is and whether there is enough food. The ascarosides thus help the worms in the population decide whether the neighborhood is good – meaning they should hang around, eat, and make babies – or whether the neighborhood is bad. If so, the worms should develop into a larval stage specialized for dispersal that will allow them to find a better neighborhood. Roundworms make the ascarosides by attaching a long chemical ‘side chain’ to an ascarylose sugar. Further chemical modifications allow the worms to produce different signals. In general, to signal a good neighborhood, worms attach a structure called an indole group to the ascarosides. To signal a bad neighborhood, worms make the side chain very short. But how does a worm control which ascarosides it makes? Zhou, Wang et al. now show that C. elegans can change the meaning of its chemical message by modifying the ascarosides that it has already produced instead of making new ones from scratch. Specifically, as their neighborhood runs out of food, C. elegans can use an enzyme called ACS-7 to initiate the shortening of the side chains of indole-ascarosides. The worm can thus change a favorable ascaroside signal that causes the worms to group together into an unfavorable ascaroside signal that causes the worms to enter their dispersal stage. Although Zhou, Wang et al. have focused on chemical communication in C. elegans, the findings could easily apply to the many other species of roundworm that produce ascarosides. Knowing how worms communicate will help us to understand how worms respond to their environment. This knowledge could potentially be used to interfere with the lifecycles and survival of parasitic worm species that harm health and crops. 

   more » « less