Stinson, Loraina et al. (2015) International Worm Meeting "Assessment of DAF-19-Related Behavioral Defects."

Stinson, Loraina, Swoboda, Peter, Sugiaman-Trapman, Debora, Piasecki, Brian P.

[International Worm Meeting, 2015]

The daf-19 gene encodes the only RFX transcription factor in C. elegans, producing at least four related protein isoforms, one of which, DAF-19C, is responsible for ciliogenesis. Previous work by Senti and Swoboda (Mol Biol Cell 2008) demonstrated that adult worms deficient in all four DAF-19 proteins have extremely aberrant dwelling and roaming behavior on food. Most intriguing is that transgenic addition of the DAF-19C isoform restored cilia formation, but did not fully restore dwelling and roaming behavioral defects. We are developing a related assay that mimics a patchy food environment to further probe worm foraging behavior. We are testing worms lacking all isoforms of DAF-19 as well as those containing mutant alleles that affect only the larger isoforms of DAF-19 to determine whether these isoforms play a role in nervous system function.

Ding, Siyu Serena et al. (2021) International Worm Meeting "Using high-throughput behavioural assays to identify heritable natural genetic variants in three Caenorhabiditis species"

Andersen, Erik C, Ding, Siyu Serena, Brown, Andre EX, Shrestha, Priyanka, Stinson, Loraina

[International Worm Meeting, 2021]

The most standard behavioural assay involves imaging worms crawling on NGM agar. Recent developments in hardware and software increase the throughput of these experiments by running multiple experimental replicates in parallel and by automating post-acquisition worm tracking and feature extraction. We imaged and analysed the crawling behaviour of 197 C. elegans wild isolates in the presence of the OP50 food source, and used genome-wide association (GWA) analyses to identify several quantitative trait loci that are linked to specific behavioural features. Additionally, we explored multiple behavioural assays involving more "challenging" environments, and found that these assays reveal more pronounced behavioural differences at the species level (between C. elegans, C. briggsae, and C. tropicalis) compared to the standard crawling assay. We plan to apply these behavioural assays to hundreds of wild isolates from the three species, in order to identify natural genetic variants that underlie heritable behavioural traits across the Caenorhabiditis genus.

Yanagi, Katherine et al. (2021) International Worm Meeting "Suppressors of stress-induced glutamatergic neuron degeneration in sod-1G85R ALS model"

Mahapatra, Animesh, Walsh, Melissa, Tsai, Jason, Hart, Anne, Lins, Jeremy, Yanagi, Katherine, Stinson, Loraina, Kruskop, Jane, Osborne, Jennifer

[International Worm Meeting, 2021]

Amyotrophic Lateral Sclerosis (ALS) is one of the most common adult-onset neurodegenerative disorders that results from the selective and progressive degeneration of cortical and spinal motor neurons. Mutations over 20 genes including RNA binding proteins, FUS and TDP43, and a free radical scavenger, superoxide dismutase 1 (SOD1) cause ALS. Although there is a well-established genetic component of ALS, it is still unclear why mutations in genes encoding functionally diverse proteins cause motor neuron degeneration. Identifying modifiers of neurodegeneration in C. elegans ALS models may provide insight into the mechanisms behind the selective and progressive neurodegeneration in ALS. Here, we have undertaken a classical forward genetic screen to identify suppressors of glutamatergic neuron degeneration. After exposure to oxidative stress, SOD-1G85R knock-in mutants have both glutamatergic and cholinergic neuron degeneration (PMC6200258). We mutagenized SOD-1G85R animals and screened for suppressors of glutamatergic neuron degeneration. After whole genome sequencing, we found that an RNA binding protein, hit in three independently isolated lines, suppresses cholinergic and glutamatergic neuron degeneration. Understanding the relationship between SOD1 and RNA binding proteins will provide insight if there are common mechanisms underlying neurodegeneration in ALS and has the potential to facilitate the development of treatments.

Crombie, Tim et al. (2021) International Worm Meeting "Repeated Sampling of Caenorhabditis elegans Across the Hawaiian Islands Reveals Spatiotemporal Patterns of Genetic Diversity"

Stevens, Lewis, Buchanan, Claire, Andersen, Erik, Stinson, Loraina, Dilks, Clayton, Tanny, Robyn, Lu, Dan, Zhang, Gaotian, Evans, Kathryn, Zdraljevic, Stefan, Crombie, Tim, Lee, Daehan, Roberto, Nicole, Wang, Ye, Cook, Daniel

[International Worm Meeting, 2021]

Caenorhabditis elegans isolated from the Hawaiian Islands are known to harbor a high degree of genetic diversity relative to non-Hawaiian isolates. It was recently suggested that Hawaiian C. elegans can be partitioned into at least four genetically distinct groups. An analysis of geospatial environmental data further suggested that the genetic groups might associate with environmental parameters such as elevation and temperature, although the sample size for that study was small (n = 43 isolates). To better characterize the niche and genetic diversity of Hawaiian C. elegans and further define the associations of genetic groups with environmental parameters, we sampled different substrates and niches across the Hawaiian Islands six times over a three-year period. In total, we isolated 7,107 nematodes from 2,400 of 4,506 substrate samples (53% success rate). Among the nematodes we isolated, we identified five Caenorhabditis species, including 499 C. elegans, 377 C. briggsae, and 55 C. tropicalis isolates. We measured several environmental parameters at each sampling site and combined them with environmental parameters from geospatial databases to reveal that C. elegans is typically found in cooler and relatively drier climates at higher elevation than the other two selfing Caenorhabditis species. We isolated C. elegans most frequently from montane-alpine mesic forest habitat dominated by plant species native to the Hawaiian Islands. When possible, we cryopreserved C. elegans isolates and sequenced their genomes. To date, including Hawaiian isolates from collaborators, we have sequenced the genomes of 505 Hawaiian C. elegans isolates. With these data, we grouped the isolates into 163 isotypes (strains belonging to a single isotype have >0.9997 genome-wide concordance). We found that some of the isotypes were collected from the same locations over the three-year sampling period, and most of the collections of the same isotype were found within 500 meters of each other. Principal component analysis (PCA) of genetic variation revealed that the 163 isotypes fall into seven genetically distinct groups, three more than previously found on the islands with a smaller sample. Taken together, our findings begin to outline the spatiotemporal patterns of C. elegans genetic diversity on the Hawaiian Islands and raise new questions about evolutionary forces driving the genetic structure we have uncovered. For example, are these groups isolated by ecological or geographic distances, or perhaps both, and to what extent do reproductive incompatibilities contribute to the structure we have observed?