Brown, Andre et al. (2017) International Worm Meeting "A common format for worm tracking data."

Kerr, Rex, Brown, Andre, Lee, Chee Wai, Hokanson, Jim, Currie, Michael

[International Worm Meeting, 2017]

Many labs, including ours, have built a wide variety of worm trackers. These have a wide range of capabilities, from high-resolution imaging of single animals during calcium imaging, to very low-resolution imaging of animals as points. This diversity of capability enables the C. elegans community to address a wide range of problems at an appropriate scale. Most of these trackers also produce some data that is very similar to that of other trackers: animal position or spine, for example. Unfortunately, each tracker uses its own format to store data, so that any later analysis, despite being general in nature, cannot be performed on data from different machines. As the volume of tracking data grows, and the variety of downstream analysis methods expands, this limitation will pose an increasingly large barrier to replication of and extension of existing work across different labs. To address this issue, we have defined the Worm Common Object Notation, a set of rules for how to write tracking data in the ubiquitous JSON format, so that it can be easily shared between labs. To facilitate easy adoption of WCON, we have further written software in a variety of languages that will read or write data in WCON format. So far, we have implementations in Python, Scala, Matlab, and Julia, and wrapper libraries for Octave, R, and Java to use one of the main implementations. Additionally, the Tracker Commons project of which WCON is a part contains a small but rapidly growing set of pre-packaged analysis tools for routine manipulation of worm tracking data. We will also maintain a list of other WCON-compatible analysis tools as they become available. If you are involved in worm tracking, we invite you to adopt WCON and help make C. elegans behavioral data widely accessible. WCON is developed under the open source Tracker Commons project of the OpenWorm Foundation. We invite contributions and improvements!

Brown, Andre E.X. et al. (2013) International Worm Meeting "A quantifiably complete repertoire of C. elegans locomotion."

Schwarz, Roland, Schafer, William, Branicky, Robyn, Brown, Andre E.X.

[International Worm Meeting, 2013]

Visible phenotypes have played a critical role in understanding the molecular basis of behaviour in model organisms. However, most current descriptions of behaviour are based on manually identified events or a limited set of quantitative parameters. Here we report an extension of the concept of behavioural motifs to exhaustively catalogue C. elegans locomotion and derive a repertoire that is quantifiably complete. A repertoire learned for spontaneous behaviour in wild-type worms can be used to fit data from mutants or worms in different environmental conditions and provides a sensitive measure of phenotypic similarity. Repertoire comparison can also be used to assess inter-individual variation and the compositionality of behaviour, that is, the extent to which behavioural adaptation involves the creation of novel repertoire elements or the reuse of existing elements in novel sequences. Repertoire derivation is general, so that given a representation of posture, our approach will apply to other organisms.

Gomez-Marin, Alex et al. (2015) International Worm Meeting "Compressibility quantifies the stereotypy and complexity of C. elegans locomotion."

Gomez-Marin, Alex, Stephens, Greg, Brown, Andre

[International Worm Meeting, 2015]

There has been increasing interest in unbiased methods for quantifying behaviour and C. elegans' simple morphology makes it a useful animal for testing new approaches. We have recently described a method of representing locomotion as a sequence of transitions between a set of discrete template postures. This makes it possible to enumerate the full variety of observed behavioural motifs in a systematic way. Here we combine the discrete representation with a hierarchical compression algorithm to quantify the complexity and stereotypy of spontaneous locomotion of a large set of mutants and wild isolates. More stereotyped, repetitive locomotion is more compressible than more random, uncoordinated behaviour. We find that most wild isolates show more stereotyped locomotion than N2, but that this difference is not explained by npr-1 since an npr-1 loss of function mutant shows behaviour that is approximately as complex as N2.

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.

Yemini, Eviatar I. et al. (2013) International Worm Meeting "A database of C. elegans behavioral phenotypes."

Brown, Andre E.X., Yemini, Eviatar I., Grundy, Laura J., Schafer, William R., Jucikas, Tadas

[International Worm Meeting, 2013]

Previous single and multi worm tracking experiments have produced summary statistics to phenotype small worm sets. We introduce a database of extensive and intensive single-worm phenotypes for over 300 strains of C. elegans with nervous system and locomotory defects as well as a reference of N2 variability composed of more than 1,200 young-adult hermaphrodites examined over the course of 3 years. The data is available online at http://wormbehavior.mrc-lmb.cam.ac.uk and includes a link to Worm Tracker 2.0 (our single-worm tracker used for data collection). Our phenomic database provides multiple levels of representation, from high-level statistical strain summaries all the way down to detailed time-series measurements for over 10,000 single-worm experiments. Within our database are 76 mutants with no previously characterized phenotype, 15 genes with multiple allelic representation, and 13 double or triple mutant combinations (the majority of which are accompanied by single mutant representation as well). Annotated experimental videos are easily accessible alongside their data, with various degrees of processing, from the skeleton and outline coordinates to the time series of extracted features, their histograms, and an in-depth view of collective strain statistics. For computational researchers, the database is a rich source of processed measures and raw data for developing new algorithms for segmentation, behavioral quantification, and bioinformatic approaches which link complex phenotypes with genetic perturbations. For neurogeneticists, the summary statistics and visualizations make it possible to identify behavioral phenotypes in mutants of interest. Free Worm Tracker 2.0 software and simple plans to build its inexpensive hardware are available at http://www.mrc-lmb.cam.ac.uk/wormtracker/.

Michael A Beer (2005) International Worm Meeting "Systematic genome-wide identification of transcriptional cis-regulatory logic in C. elegans."

Michael A Beer

[International Worm Meeting, 2005]

We have developed a systematic approach for inferring cis-regulatory logic from whole-genome microarray expression data.[1] This approach identifies local DNA sequence elements and the combinatorial and positional constraints that determine their context-dependent role in transcriptional regulation. We use a Bayesian probabilistic framework that relates general DNA sequence features to mRNA expression patterns. By breaking the expression data into training and test sets of genes, we are able to evaluate the predictive accuracy of our inferred Bayesian network. Applied to S. cerevisiae, our inferred combinatorial regulatory rules correctly predict expression patterns for most of the genes. Applied to microarray data from C. elegans[2], we identify novel regulatory elements and combinatorial rules that control the phased temporal expression of transcription factors, histones, and germline specific genes during embryonic and larval development. While many of the DNA elements we find in S. cerevisiae are known transcription factor binding sites, the vast majority of the DNA elements we find in C. elegans and the inferred regulatory rules are novel, and provide focused mechanistic hypotheses for experimental validation. Successful DNA element detection is a limiting factor in our ability to infer predictive combinatorial rules, and the larger regulatory regions in C. elegans make this more challenging than in yeast. Here we extend our previous algorithm to explicitly use conservation of regulatory regions in C. briggsae to focus the search for DNA elements. In addition, we expand the range of regulatory programs we identify by applying to more diverse microarray datasets.[3] 1. Beer MA and Tavazoie S. Cell 117, 185-198 (2004). 2. Baugh LR, Hill AA, Slonim DK, Brown EL, and Hunter, CP. Development 130, 889-900 (2003); Hill AA, Hunter CP, Tsung BT, Tucker-Kellogg G, and Brown EL. Science 290, 809812 (2000). 3. Baugh LR, Hill AA, Claggett JM, Hill-Harfe K, Wen JC, Slonim DK, Brown EL, and Hunter, CP. Development 132, 1843-1854 (2005); Murphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, Ahringer J, Li H, and Kenyon C. Nature 424 277-283 (2003); Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley R, Jones SJ, Davis EB, Scherer S, Ward S, and Kim SK. Mol Cell 6 605-616 (2000).

Erich M Schwarz et al. (2003) International Worm Meeting "Comparative analysis of cis-regulatory sequences using four Caenorhabditis species."

Nora Mullaney, Erich M Schwarz, Tristan De Buysscher, Paul W Sternberg, Barbara J Wold, John A DeModena, Eunpyo Moon, Hiroaki Shizuya

[International Worm Meeting, 2003]

Comparing homologous cis-regulatory DNA sequences from three or more genomes has advantages over pairwise comparison of only two. Cis-regulatory sequences are short (6-20 bp) and tolerate substantial variation. Purely random pairing of unrelated 100-bp DNA segments is expected to yield two perfect 6 bp matches. Alignment of a third or fourth sequence should greatly lower the frequency of false positive regions, allowing small but real cis-regulatory sequences to be efficiently detected. This increased resolution should also allow direct comparison between phylogenetically conserved sequences and statistically overrepresented sequences, which may yield complementary views of regulatory elements. In the Caenorhabditis genus, C. remanei appears to be most closely related to C. briggsae; two other species, CB5161 and PS1010, comprise the two closest known and culturable Caenorhabditis species outside the elegans-briggsae group (Fitch, 2000). CB5161 is closest to C. elegans, and PS1010 the next most divergent; these two species thus provide an evolutionarily graded series. We have constructed fosmid libraries from CB5161 and PS1010, and begun sequencing individual fosmids for comparative analysis of genes involved in vulval or sensory neuron development. At the same time, we have devised the Mussa software package to adapt the algorithms of Davidson and coworkers (Brown et al., 2002) to multiple sequence analysis. At this writing, we have sequence data from the egl-30, lin-11, and mab-5 loci of both CB5161 and PS1010. Initial results of sequencing and comparative sequence analysis will be presented. References: Brown, C.T., Rust, A.G., Clarke, P.J., Pan, Z., Schilstra, M.J., De Buysscher, T., Griffin, G., Wold, B.J., Cameron, R.A., Davidson, E.H., and Bolouri, H. (2002). New computational approaches for analysis of cis-regulatory networks. Dev. Biol. 246, 86-102; Fitch, D.H.A. (2000). Evolution of Rhabditidae and the male tail. J. Nematol. 32, 235-244.

Jens Schulze et al. (2007) International Worm Meeting "Cytoplasmic segregation, interphase MT and establishment of cell polarity in the embryo of the basal nematode R. culicivorax."

Einhard Schierenberg, Jens Schulze

[International Worm Meeting, 2007]

One of the central questions for developmental biologists is how cellular polarity is established and leads to blastomeres with different fate. We study nematodes from various phylogenetic positions in comparison to C. elegans in order to assess variations in the pattern of embryonic development. One of our study objects, the more basal species Romanomermis culicivorax, shows peculiarities with respect to cell polarity not observed in any other nematode. Due to differences in the orientation of cleavage spindles spatial pattern formation in R. culicivorax differs markedly from that in C. elegans. Blastomeres which in C. elegans perform a transverse, equal cleavage divide unequally with an a-p spindle orientation and vice versa. In addition, we find - so far unique among nematodes - that colored cytoplasm is segregated into a single blastomere (EMS) which inherits it to all of its descendants. Furthermore, as another phenomenon, to our knowledge not described in other animal systems, during interphase microtubule caps form in specific regions of the cortex which disappear prior to mitosis. We find these caps predominantly in cells destined to execute polar divisions indicating their involvement in cell polarisation. The EMS cell containing the brown pigment, will divide into equal left and right daughters and is the only 4-cell blastomere without interphase MT caps. Our data demonstrate that developmental variations among nematodes are more prominent and abundant than anticipated so far.

Schlosser, A. et al. (2015) International Worm Meeting "Chronic exposure to pesticide residues exacerbates alpha-synuclein pathology in a Caenorhabditis elegans Parkinson's disease model."

Flaherty, D., Schlosser, A., Davis, M.

[International Worm Meeting, 2015]

Human health issues and disease have long been linked to environmental exposures which may be the greatest risk factors for the development of neurodegenerative diseases (Franco et al. 2010). Epidemiological studies show that exposure to environmental agents such as pesticides is a key contributor to the development and exacerbation of Parkinson's Disease (PD) (Franco et al. 2010). Intraneuronal inclusions, known as Lewy bodies, composed primarily of aggregated alpha-synuclein, are the primary causative formations associated with the loss of dopaminergic neurons and the development of PD (Baltazar et al. 2014; Brown et al. 2006). The loss of these neurons causes dysfunction of the basal ganglia and the subsequent inhibition of motor control, the defining characteristic of the disease (Baltazar et al. 2014). This study looks to assess the possible toxicological effects of chronic exposure to three common pesticides, chlorpyrifos, carbaryl and indoxacarb, at maximum tolerated residue levels set by the Environmental Protection Agency (EPA) in a Caenorhabditis elegans PD model. While the EPA employs strict regulations on individual pesticides, there are no regulations governing the mixing of pesticides. In this study, pesticides are tested both individually and as binary mixtures in order to investigate alpha-synuclein toxicity. Results from the study indicate that individually, these pesticides, with the exception of indoxacarb, have a noticeable effect on alpha-synuclein pathology. When combined to form binary mixtures, all pesticides have a drastic effect on alpha-synuclein pathology and mortality, despite being within EPA limits.

Brockett, Mary et al. (2015) International Worm Meeting "Virulence of a Novel Melanin Producing Pseudomonas Species UC17F4 on Caenorhabditis elegans."

Brockett, Mary, Morreale, Meghan, Aaronson, Lawrence, Shinn-Thomas, Jessica

[International Worm Meeting, 2015]

Pseudomonas sp. UC17F4 is a novel species of Pseudomonas isolated in our lab from the cutaneous microbial flora of the red-backed salamander, Plethodon cinereus. UC17F4 produces intracellular melanin, a brown pigment, in the presence of tyrosine-rich media. Melanin has been shown to serve as a virulence factor for several organisms, including bacteria and fungi. Our lab generated several mutant strains of UC17F4: UC17F4 (MM1) produces less melanin than the wild-type strain, UC17F4 (MM7, 8, and 9) hypersecrete extracellular melanin, and UC17F4 (PV 21 and 22) produce no melanin. We demonstrated that UC17F4 exhibits virulence by using C. elegans as a model host. Worms were transferred to lawns of UC17F4 bacteria on Nematode Growth Media (NGM) supplemented with tyrosine and lethality was assessed over time using touch assays. Our studies show that C. elegans exposed to the wild-type strain (UC17F4) have the highest mortality rate and worms exposed to UC17F4 (PV21) have the lowest mortality. Worms do not die after exposure to the hypersecreting strains or the strains without melanin. We investigated the effect of UC17F4 exposure on the different larval stages of C. elegans (L1, L2, L3, L4, and adult worms). Our results show that L1 and L2 worms are most vulnerable to the virulence of UC17F4 compared to later developmental stages. L1 and L2 worms die in less than 24 hours of exposure, whereas later developmental stages are viable and reproduce. Our current studies include determining the kinetics of L1 and L2 lethality using both touch assays and in vivo fluorescent cell death assays (SYTOX®) in a microplate reader, and determining the mode of pathogenesis using high-magnification light microscopy to examine the anatomical areas of melanin and UC17F4 biofilm accumulation. .