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.

Yamazaki, S. et al. (2017) International Worm Meeting "Learning-dependent behavioral modulation of sensory behavior revealed by machine learning and optophysiological analysis in a virtual environment."

Ikejiri, Y., Hiramatsu, F., Yamazaki, S., Fujita, K., Kimura, K., Tanimoto, Y., Hashimoto, K., Maekawa, T., Yamazoe-Umemoto, A.

[International Worm Meeting, 2017]

Animals modify their behavior based on experiences as learning, although identifying component(s) of behavior modulated by learning has been difficult. In contrast to neural activities, which can be monitored in large numbers of cells simultaneously recently, behavior in general is still analyzed in classic ways and insufficiently studied using simple measures, such as velocity, migratory distance, and/or the probability of selecting a particular goal. Comprehensive classifications of animals' behavior by using machine vision and machine learning methods have been achieved (Gomez-Marin et al., Nat Neurosci, 2014; Brown et al., PNAS, 2013). However, these methods have not been applied to animals' sensory behavior because of technical limitations in measuring sensory signals that animals receive during the behavior. To overcome this problem and effectively identify behavioral components modulated by learning, we used machine learning aiming to detect changes in navigation of worms in a measured odor gradient. We have previously reported that, after experiencing the repulsive odor 2-nonanone for 1 h, worm's odor avoidance behavior is enhanced, and that they move away from the odor source more efficiently (Kimura et al., J Neurosci, 2010). We have also quantified the dynamic changes in the odor concentration during odor avoidance behavior (Yamazoe-Umemoto et al., Neurosci Res, 2015). In the present study, we used decision tree, a machine learning algorithm, to extract features of the animal's sensorimotor response during navigation modified by odor learning. During the migration down the odor gradient, naive worms responded to slight increases in the repulsive odor concentration by stopping forward movements and initiating turns. In contrast, the probability of response was lowered after learning, suggesting that the learned worms ignore "a yellow light". Consistently, by calcium imaging of ASH neurons, whose activation causes turns under a virtual odor gradient (Tanimoto et al., this meeting), we found that the ASH response to a small increase in the odor concentration was reduced after learning. Furthermore, by applying the decision tree analysis, multiple mutant strains were categorized into several groups based on behavioral features. Thus, the integrative machine learning analysis of sensory information and behavioral response is a powerful tool to obtain comprehensive understanding of dynamic activities of neural circuits and its modulation by learning.

Sarfarazhussain Farooqui et al. (2006) European Worm Meeting "A GFP Reporter Based Screen for the Notch Target Genes during Vulval Development"

Sarfarazhussain Farooqui, ALEX HAJNAL, Ivo Rimann

[European Worm Meeting, 2006]

Sarfarazhussain Farooqui, Ivo Rimann and Alex Hajnal. During hermaphrodite vulval development, lateral signaling from the primary vulval precursor cell (VPC) P6.p activates the LIN-12 Notch pathway in the neighbouring secondary VPCs P5.p and P7.p. The LIN-12 Notch signal inhibits primary fate specification and promotes the secondary vulval fate by activating transcription factors of the CSL family, which turn on the expression of specific target genes.. LIN-12 Notch targets usually contain clusters of CSL binding sites (RTGGGAA) in their promoter/enhancer regions. To identify new target genes of the LIN-12 Notch pathway in a systematic way, we searched the C. elegans genome sequence for genes containing clusters of three or more CSL sites within 2 kbp upstream of the start codon. We further refined our list of candidate Notch targets by taking into consideration only those genes in which the putative CSL sites are conserved in the C. briggsae orthologs. Promoter-GFP fusion constructs for the 23 strongest candidate genes were made by fusion PCR and injected into wild-type worms to create transgenic lines. Details on the expression patterns of the reporter constructs generated so far will be presented at the meeting.

Tauffenberger, Arnaud et al. (2009) International Worm Meeting "Age-dependent modification of expanded CAG toxicity in simple C. elegans models."

Parker, Alex, Tauffenberger, Arnaud, Bel-Hadj, Samar

[International Worm Meeting, 2009]

Arnaud Tauffenberger1,2,3, Samar Bel-Hadj1, Alex Parker1,2, 3 1CRCHUM, 2Centre of Excellence in Neuromics, 3Department de pathologie et biologie cellulaire, Universite da Montreal, Montreal, Quebec, Canada The expansion of CAG trinucleotides coding for glutamine is the cause of at least nine late-onset neurodegenerative diseases. The expanded CAG (expCAG) diseases may have some pathogenic mechanisms in common as the disease threshold for all of these disorders is around 40 CAG repeats and they display misfolded intracellular protein aggregation phenotypes. We have turned to the model organism C. elegans to explore two areas of interest: 1. Age-dependent toxicity: Although the expCAG diseases show anticipation, the size of CAG repeat only partially correlates with the variation in age-of-onset. Evidence suggests that even for these single trait neurodegenerative diseases, disease onset and progression may have additional environmental and genetic components. Using C. elegans transgenic worms expressing expCAG in neurons we are exploring the links between aging and late-onset neurodegeneration. We hypothesize that genes regulating longevity, stress response, their associated signaling pathways and downstream effectors may encode new therapeutic targets for age-dependent proteotoxicity in humans. 2. Mechanisms of expCAG toxicity: Long homopolymeric CAG nucleotide stretches are unstable and may be prone to translation errors. Mistranslation of expCAG to alternate reading frames may produce hybrid proteins with additional toxicity. We have created transgenic strains to investigate this phenomenon. A summary of our data and recent findings will be presented.

Lee, J. et al. (2019) International Worm Meeting "Y92H12A.4(ints-3), a subunit of the Integrator complex, acts in AFD thermosensory neurons to support a behavioral preference."

Almoril-Porras, A., Colon-Ramos, D., Lee, J., Hawk, J.

[International Worm Meeting, 2019]

A fundamental question in neuroscience is to elucidate the cellular and molecular changes that occur during learning. To address this, we are using C. elegans thermotaxis behavior as a model to identify molecules that play a role in learning. C. elegans does not have an innate preferred temperature; instead, worms will migrate on a thermal gradient toward their previously experienced temperature conditions. Previously, PKC-1 has been identified as a key molecule that bidirectionally regulates temperature preference independent of experience: pkc-1(lof) animals are constitutively thermophilic, while pkc-1(gof) animals are constitutively cryophilic (Okochi et al. 2005). In order to identify interactors of PKC-1, we conducted a forward mutagenesis screen on pkc-1(gof) animals and isolated one allele, ola295, that robustly suppressed their constitutively cryophilic behavior. Using SNP mapping, whole genome sequencing, and CRISPR rescue, we identified ola295 as a nonsense allele of Y92H12A.4(ints-3), a subunit of the Integrator complex, which was recently shown in C. elegans to play a conserved role in small nuclear RNA (snRNA) processing (Gomez-Orte et al. 2019). Cell-specific rescue experiments suggest Y92H12A.4 acts in AFD thermosensory neurons to support the constitutive cryophilic behavior of pkc-1(gof) animals. Y92H12A.4(ola295) animals show decreased GCaMP amplitudes in AFD neurons and an increased response penetrance in the postsynaptic AIY neurons in response to temperature stimuli, suggesting that the allele results in the disinhibition of AIY neurons to suppress pkc-1(gof) cryophilic behavior. We are now investigating whether this suppression arises from a shift in the gain of AFD sensory responses through snRNA-dependent mechanisms.

Ivo Rimann et al. (2006) European Worm Meeting "The Transcription Factor EGL-43 is Necessary for Anchor Cell Invasion during Vulval Development"

Ivo Rimann, ALEX HAJNAL

[European Worm Meeting, 2006]

Ivo Rimann and Alex Hajnal. For proper egg-laying by the hermaphrodite, the uterus has to become firmly connected to the vulva during late larval development. The anchor cell (AC), a specialized cell in the somatic gonad, coordinates vulval and uterus development and initiates the formation of the connection between these two tissues.. During the L3 larval stage, the AC induces six neighboring ventral uterine (VU) cells to adopt the Pi cell fate. Around the same time of development, the basal laminas separating the uterus from the vulva begin to dissolve and the AC invades the vulval tissue by extending a process between the primary cells (Sherwood et al., 2003). In this way, the AC connects the vulval and uterine tissues.. In an RNAi-based screen for genes regulating vulval morphogenesis, we have found that knock-down of egl-43 causes a penetrant protruding vulva (Pvl) phenotype because the connection between the uterus and vulva is not formed correctly. egl-43 encodes a zinc finger transcription factor homologous to the human EVI1 proto-oncogene. Closer examination showed that in egl-43 RNAi animals the basal lamina under the AC is not removed, which prevents the AC from invading the vulval tissue. In addition, egl-43 RNAi animals show defects in the specification of the Pi cell fate. Similar defects in AC invasion have been reported for fos-1 mutants (Sherwood et al., 2005), and like fos-1, a transcriptional egl-43p::gfp reporter is expressed at high levels in the AC and at lower levels in the adjacent VU cells. Moreover, egl-43p::gfp expression in the AC is 5-fold reduced in a fos-1(0) background, indicating that FOS-1 promotes AC invasion at least in part by up-regulating egl-43 expression in the AC.

REMY J.J. (2003) International Worm Meeting "LONG TERM MEMORY OF THE NATAL CHEMOSENSORY WORLD IN NEMATODES"

REMY J.J.

[International Worm Meeting, 2003]

The nematode C. elegans rely on a limited number of neurons to sense chemicals, each of it expressing several G-coupled chemoreceptors out of more than 800 found in the genome. Since neurons direct behavior and not the receptors they express, worm responses to chemicals will depend on the chemoreceptors expression pattern in the different chemosensory neurons. As in other species, expression of these genes in nematodes can start very early during development, before they play their role in adult sensing and behavior. We found different strains of C. elegans able to stay sensitized to odorants to which they have been shortly exposed from embryogenesis to the L1 larval stage. Sensitization by early exposure must be food or serotonine associated and lasts for the whole reproductive life. It is however not erasable by starvation at the adult stage. This form of experience-dependent sensory adaptation can be highly specific for different odorants concentrations, even if they are sensed by the same olfactory neuron, and is significantly enhanced in daf-22(ml30) worms that does not secrete pheromone, the only known repressor of chemoreceptor expression (1). By contrast, the sensory processing interneurone AIY seems necessary since the two ttx-3(ot22) and ttx-3(ks5) mutants (2) were found defective for odor imprinting, as were found the themosensory mutants sel-12(ar131), sel-12(ar171), and ncs-1(qa406) (3, 4). All together, these data suggest that the nematode natal chemosensory world can be permanently imprinted, if food or serotonine associated, possibly through ligand-dependent chemoreceptors expression mechanisms. The biological significance of this form of sensory plasticity will be discussed. 1) Peckol EL et al., PNAS 2001, 98, 11032-11038 2) Hobert O et al., Neuron 1997, 19, 345-357 3) Levitan D and Greenwald I. Nature 1995, 377, 351-4 4) Gomez M et al., Neuron 2001, 30, 241-248

Xiong, R. et al. (2019) International Worm Meeting "Cellular and molecular mechanisms of mok-1 function in left-right neuronal asymmetry."

Xiong, R., Chuang, C.-F., Wang, X.

[International Worm Meeting, 2019]

The developing nervous system generates a large diversity of cell types with distinct patterns of gene expression and functions. One way to establish neuronal diversity is to specify neuronal subtypes across the left-right axis. The C. elegansleft and right AWC olfactory neurons communicate to specify asymmetric subtypes, AWCOFF and AWCON. The default AWCOFF is specified by a Ca2+-regulated kinase cascade that is activated by influx of Ca2+ through the voltage-gated Ca2+ channel UNC-2/UNC-36. Intercellular communication between the two AWC neurons and other neurons through the NSY-5/innexin gap junction network antagonizes unc-2/unc-36 Ca2+ signaling in the induced AWCON cell. Our recent data suggest that voltage- and calcium-activated SLO BK potassium channels slo-1and slo-2acts redundantly downstream of nsy-5 to inhibit unc-2/unc-36 Ca2+ signaling in the specification of AWCON. To identify the genes required for slo-1function in inhibiting unc-2/unc-36 Ca2+ signaling for promoting AWCON, we performed a non-biased forward genetic screen to isolate mok (modifier of K+ channel) mutants that suppress the slo-1(gf) 2AWCON phenotype. mok-1(vy11) is one of the mutants identified from this screen. The 2AWCOFF phenotype of mok-1(vy11) mutants is suppressed by loss-of-function mutations in the Ca2+ channel gene unc-36, suggesting that mok-1 acts upstream of the unc-2/unc-36 Ca2+ signaling pathway. Together, our results suggest a model in which nsy-5 inhibits unc-2/unc-36 Ca2+ signaling through slo-1 and mok-1. We identified the mutation responsible for the vy11 phenotype using whole genome sequencing with the help of Alex Boyanov in the Oliver Hobert lab. Further genetic analysis and behavior analysis of the vy11 mutant, as well as molecular characterization of mok-1 will be presented in the meeting.

Wang D et al. (2019) IEEE Access "Cellular structure image classification with small targeted training samples."

Bao Z, Xu Y, Santella A, Wang D, Lu Z, Wang ZI

[IEEE Access, 2019]

Cell shapes provide crucial biological information on complex tissues. Different cell types often have distinct cell shapes, and collective shape changes usually indicate morphogenetic events and mechanisms. The identification and detection of collective cell shape changes in an extensive collection of 3D time-lapse images of complex tissues is an important step in assaying such mechanisms but is a tedious and time-consuming task. Machine learning provides new opportunities to automatically detect cell shape changes. However, it is challenging to generate sufficient training samples for pattern identification through deep learning because of a limited amount of images and annotations. We present a deep learning approach with minimal well-annotated training samples and apply it to identify multicellular rosettes from 3D live images of the <i>Caenorhabditis elegans</i> embryo with fluorescently labeled cell membranes. Our strategy is to combine two approaches, namely, feature transfer and generative adversarial networks (GANs), to boost image classification with small training samples. Specifically, we use a GAN framework and conduct an unsupervised training to capture the general characteristics of cell membrane images with 11,250 unlabelled images. We then transfer the structure of the GAN discriminator into a new Alex-style neural network for further learning with several dozen labeled samples. Our experiments showed that with 10-15 well-labeled rosette images and 30-40 randomly selected nonrosette images our approach can identify rosettes with more than 80% accuracy and capture more than 90% of the model accuracy achieved with a training data et that is five times larger. We also established a public benchmark dataset for rosette detection. This GAN-based transfer approach can be applied to the study of other cellular structures with minimal training samples.

Claudia Walser et al. (2006) European Worm Meeting "Distinct Roles of the Pumilio and FBF Translational Repressors during C. elegans Vulval Development"

Gopal Battu, ALEX HAJNAL, Claudia Walser, Erika Frohli Hoier

[European Worm Meeting, 2006]

Claudia Walser, Gopal Battu, Erika Frhli Hoier and Alex Hajnal. Members of the conserved PUF (Pumilio and FBF repeat) protein family regulate various aspects of germ line development by selectively binding to the 3 untranslated region of their target mRNAs and repressing translation. FBF-1 and FBF-2 regulate the sperm/oocyte switch and mitosis versus meiosis decision by repressing fem-3 and gld-1 translation, respectively (Zhang et al., 1997; Crittenden et al., 2002). We found that puf-8, fbf-1 and fbf-2 also act in the soma where they negatively regulate vulval development.. Loss-of-function mutations in puf-8 cause excess vulval differentiation when combined with mutations in negative regulators of the EGFR/RAS/MAPK pathway, and they suppress the Vulvaless phenotype caused by mutations that reduce EGFR/RAS/MAPK signaling. A PUF-8::GFP translational reporter is initially expressed in all six vulval precursor cells (the VPCs P3.p through P8.p) but gets restricted to the distal, uninduced (3) VPCs after vulval fate specification. Moreover, the fusion of the distal VPCs to the hypodermal syncytium is retarded in puf-8(lf) mutants. Thus, PUF-8 acts cell-autonomously to limit the temporal competence of the vulval precursor cells to respond to the extrinsic patterning signals. fbf-1 and fbf-2, on the other hand, function as redundant inhibitors of vulval cell fate specification in a distinct pathway that involves the repression of gld-1 translation. fbf-1 fbf-2 double mutants show ectopic 1 cell fate marker expression in adjacent VPCs. We conclude that the FBFs ensure that only one VPC (P6.p) is selected for the 1 cell fate.. Therefore, the PUF family translational repressors regulate various aspects of cell fate specification in the soma, and they may play a conserved role in modulating signal transduction during animal development.