Pritz, Christian et al. (2021) International Worm Meeting "Principles for coding associative memories in a compact neural network"

Zaslaver, Alon, Pritz, Christian, Gritsenko, Vladimir, Azulay, Aharon, Menasherof, Mai, Bokman, Eduard, Itskovits, Eyal, Nelken, Tal, Ruach, Rotem

[International Worm Meeting, 2021]

A major goal in neuroscience is to elucidate the principles by which memories are stored in a neural network. Here, we have systematically studied how the four types of olfactory associative memories (short- and long-term memories, each as positive and negative associations) are encoded within the compact neural network of C. elegans worms. By combining these robust training paradigms with fast confocal calcium imaging using multi-neuron and whole-brain imaging approaches, we systematically traced experience-dependent activity changes down to the level of individual neurites. Interestingly, short-term, but not long-term, memory broadly altered memory-evoked responses of chemosensory neurons. Modulated activity in three neurons, namely AWA, AWC, and ASE, sufficed to discriminate between the different memory states. This economy in memory-coding neurons increases memory capacity and limits non-innate behavioral responses. In contrast, long-term memory was relegated to deeper layers of the network. Primary interneurons, AIY and AIA, exhibit memory-state-dependent activation signatures, allowing the sensory system to resume innate functionality. In conclusion, olfactory associative memory appears to follow a hierarchical and temporally structured encoding logic.

Bokman, Eduard et al. (2021) International Worm Meeting "Encoding principles of a compact sensory system"

Bokman, Eduard, Pritz, Christian, Zaslaver, Alon

[International Worm Meeting, 2021]

Animals critically depend on accurate sensation and processing of environmental cues. This task becomes particularly challenging for animals with a compact and highly interconnected sensory system. Here, we used Caenorhabditis elegans nematodes to investigate how sensory information is encoded within a small nervous system. For this, we generated a strain expressing the genetically encoded calcium indicator GCaMP in all 60 ciliated neurons, and used a fast-scanning confocal system to measure activity simultaneously from all chemosensory neurons while subjecting the worms to various stimuli. We found that the sensory system responds with small, unique, and near-perfectly bi-laterally symmetrical subsets of neurons. Analysis of mutants, defective in neuro-transmitter or neuro-peptide release, revealed that the number of primary neurons which directly respond to the cue is minimal, typically consisting of 2-3 neuron types. These neurons exhibit a range of response dynamics that is both stimulus- and circuitry-dependent, effectively increasing encoding capacity of the compact sensory system. Finally, exposing animals to odor mixtures revealed that the sensory system employs a variety of logic gates including AND, OR, XOR, and NAND to process complex stimuli. Together, here we elucidated the principles that allow a small and compact sensory system to expand its encoding repertoire and to efficiently extract information from the environment.

Bokman, Eduard et al. (2019) International Worm Meeting "Encoding principles of a compact sensory system."

Ruach, Rotem, Itskovits, Eyal, Zaslaver, Alon, Pritz, Christian, Bokman, Eduard

[International Worm Meeting, 2019]

Animals critically depend on accurate sensation and processing of environmental cues. This task becomes particularly challenging for animals with a small and highly interconnected sensory system. Here, we used Caenorhabditis elegans nematodes to investigate how information is encoded within a compact sensory system. For this, we generated a new strain expressing the genetically encoded calcium indicator GCaMP in all 60 ciliated neurons, and used a fast-scanning confocal system to measure activity simultaneously from all chemosensory neurons while subjecting the worms to various stimuli. We found that the sensory system responds with small, unique, and mostly bi-laterally symmetrical subsets of neurons. Moreover, analysis of mutants, defective in neuro-transmitter or neuro-peptide release, revealed that the number of primary neurons, which directly respond to the cue, is minimal, typically comprised of 2-3 neuron types. Interestingly, these neurons exhibit a range of response dynamics that is both stimulus and circuitry-dependent, effectively increasing encoding capacity of the compact sensory system. Finally, exposing animals to combinations of stimuli revealed that the sensory system integrates information using a simple weighted sum strategy. These findings elucidate the principles that allow a small and compact sensory system to expand its encoding repertoire and to efficiently extract information from the environment.

Ruach, Rotem et al. (2019) International Worm Meeting "Irrational behavior in C. elegans arises due to asymmetric modulatory effects between options."

Iwanir, Shachar, Zaslaver, Alon, Eyal, Itskovits, Bokman, Eduard, Ruach, Rotem, Pritz, Christian

[International Worm Meeting, 2019]

Animals, like humans, repeatedly violate rational-choice paradigms, yet the underlying reasons remain debatable. This is primarily because population variability, past experience, current state, and future expectations affect decision-making cognitive processes, thus precluding decisive conclusions. Here, we established C. elegans nematodes as a powerful model for studying rationality of an innate behavior - chemotaxis, thus overcoming many of the above confounding effects. Moreover, innate behaviors presumably evolved to comply with rational economic axioms to maximize fitness. Surprisingly, we found that worms' chemotaxis behavior robustly violates key rationality paradigms of transitivity, independence of irrelevant alternatives and regularity. These violations arise due to asymmetric modulatory effects between the presented options. Functional analysis of the entire chemosensory system at a single-neuron resolution, coupled with analyses of mutants, defective in individual neurons, reveals that these asymmetric effects originate in specific sensory neurons. Thus, asymmetric modulations between options' representations may provide a simple explanation for irrational behavior.

Julien Mouysset et al. (2006) European Worm Meeting "A Conserved Role of C. elegans CDC-48 in ER-Associated Protein Degradation"

Christian Kahler, Thorsten Hoppe, Julien Mouysset

[European Worm Meeting, 2006]

Julien Mouysset, Christian Khler and Thorsten Hoppe. Protein degradation mediated by the ubiquitin/proteasome system is essential for the elimination of misfolded proteins from the endoplasmic reticulum (ER) to adapt to ER stress. It has been reported that the AAA ATPase p97/VCP/CDC48 is required in this pathway for protein dislocation across the ER membrane and subsequent ubiquitin dependent degradation by the 26S proteasome in the cytosol. Throughout ER-associated protein degradation, p97 cooperates with a binary Ufd1/Npl4-complex. In Caenorhabditis elegans two homologs of p97, designated CDC-48.1 and CDC-48.2, exist. Our results indicate that both p97 homologs interact with UFD-1/NPL-4 in a similar CDC-48UFD-1/NPL-4 complex. RNAi mediated depletion of the corresponding genes induces ER stress resulting in hypersensitivity to conditions which induce increased levels of unfolded proteins in the ER lumen. Together, these data suggest an evolutionarily conserved retro-translocation machinery at the endoplasmic reticulum.

Jacques Pecreaux et al. (2006) European Worm Meeting "Mechanical Oscillations during Asymmetric Spindle Positioning Require a Threshold Number of Active Cortical Force Generators"

Anthony A. Hyman, Stephan W. Grill, Jens-Christian Roper, Jonathon Howard, Karsten Kruse, Jacques Pecreaux, Frank Julicher

[European Worm Meeting, 2006]

Jacques Pecreaux1, Jens-Christian Rper2, Karsten Kruse3, Frank Julicher3, Anthony A. Hyman1, Stephan W. Grill, Jonathon Howard1 Background. Asymmetric division of the C. elegans zygote is due to the posterior-directed movement of the mitotic spindle during metaphase and anaphase. During this movement along the anterior-posterior axis, the spindle oscillates transversely. A theoretical analysis indicates that oscillations might occur as a result of the concerted action of many cortical force generators that pull on astral microtubules in a tug-of-war situation. This model predicts a threshold of motor activity below which no oscillations occur. Results: We have tested the existence of a threshold by using RNA interference to gradually reduce the levels of GPR-1 and GPR-2 that are involved in the G-protein-mediated regulation of the force generators. We found an abrupt cessation of oscillations as expected if the activity drops below a threshold. Furthermore, we could account for the complex choreography of the mitotic spindle - the precise temporal coordination of the build-up and die-down of the transverse oscillations with the posterior displacement - by a gradual increase in the processivity of the force generators during metaphase and anaphase. Conclusions: The agreement between our results and modeling suggests that the same motor machinery underlies two different spindle motions in the embryo: the equal and opposite motors on each side of the AP axis drive oscillations whereas the imbalanced motors in the two halves of the embryo drive posterior displacement.

Kamat, Shaunak et al. (2013) International Worm Meeting "Modulation of mec-10(d)-induced necrosis by ER chaperone NRA-2."

Kamat, Shaunak, Driscoll, Monica, Yeola, Shrutika, Bianchi, Laura

[International Worm Meeting, 2013]

ER chaperones play a major role in cellular homeostasis by regulating the assembly of polypeptides, intracellular Ca2+ signaling, and degradation of misfolded proteins. Here we report on an ER - resident chaperone NRA-2 that modulates hyper-activated ion channel-induced necrosis by regulating surface expression of a death-inducing DEG/ENaC channel family member subunit MEC-10(d). nra-2 was previously identified in a screen for nicotinic acetylcholine receptor (nAChR) - interacting proteins and was found to regulate the subunit composition of the AChR receptor in C. elegans muscle1. We found that loss of function of nra-2 led to a significant increase in mec-10(d) - induced necrosis in C. elegans touch receptor neurons (TRNs), and this enhancement was rescued by TRN-specific transgenic expression of nra-2. We observed that loss of nra-2 led to a significant increase in surface localization of MEC-10(d)::GFP and a significant decrease in ER localization. Electrophysiological experiments in Xenopus oocytes revealed that NRA-2 suppresses amiloride-sensitive currents induced by hyperactivated MEC channels. Our study suggests a role for NRA-2 as an ER quality control protein that inhibits surface expression of mutant MEC-10(d) channels and is thus neuroprotective against hyperactivated ion channel-induced necrosis. 1. Ruta B. Almedom, Jana F. Liewald, Guillermina Hernando, Christian Schultheis, Diego Rayes, Jie Pan, Thorsten Schedletzky, Harald Hutter, Cecilia Bouzat, and Alexander Gottschalk. An ER-resident membrane protein complex regulates nicotinic acetylcholine receptor subunit composition at the synapse. The EMBO Journal, 28(17):2636-2649, July 2009.

Blaxter, Mark et al. (2015) International Worm Meeting "The Caenorhabditis Genomes Project."

Stevens, Lewis, Chandrasekar, Sinduja, Koutsovoulos, Georgios, Blaxter, Mark

[International Worm Meeting, 2015]

The sequencing of the genome of Caenorhabditis elegans remains one of the milestones of modern biology, and this genome sequence is the essential backdrop to a vast body of work on this key model organism. "Nothing in biology makes sense except in the light of evolution" (Dobzhansky) and thus it is clear that complete understanding of C. elegans will only be achieved when it is placed in an evolutionary context. While several additional Caenorhabditis genomes have been published or made available, a recent surge in the number of available species in culture makes the determination of the genomes of all the species in the genus a timely and rewarding project.We have initiated the Caenorhabditis Genomes Project. From material supplied by collaborators we have so far generated raw Illumina short-insert data for sixteen species. Where possible we have also generated mixed stage stranded RNASeq data for annotation. The data are being made publicly available as early as possible (warts-and-all) through a dedicated genome website at htttp://caenorhabditis.bio.ed.ac.uk, and completed genomes and annotations will be deposited in WormBase as mature assemblies emerge. We welcome additional collaborators to the CGP, whether to assemble new genomes or to delve into the evolutionary history of favourite gene sets and systems.Species sequenced thus far in Edinburgh: Caenorhabditis afra, Caenorhabditis castelli, Caenorhabditis doughertyi, Caenorhabditis guadeloupensis, Caenorhabditis macrosperma, Caenorhabditis nouraguensis, Caenorhabditis plicata, Caenorhabditis virilis, Caenorhabditis wallacei, Caenorhabditis sp. 1, Caenorhabditis sp. 5, Caenorhabditis sp. 21, Caenorhabditis sp. 26, Caenorhabditis sp. 31, Caenorhabditis sp. 32, Caenorhabditis sp. 38, Caenorhabditis sp. 39, Caenorhabditis sp. 40, Caenorhabditis sp. 43.[Samples have been supplied by Aurelien Richaud, Marie-Anne Felix, Christian Braendle, Michael Alion, Piero Lamelza].

Karen Erbguth et al. (2009) European Worm Neurobiology Meeting "Applying and combining optogenetic and imaging tools in the C.elegans nervous system."

Martin Brauner, Alexander Gottschalk, Karen Erbguth

[European Worm Neurobiology Meeting, 2009]

Stimuli are evaluated and an animal responds to them with an appropriate behavior. How behavior is guided by neuronal circuits is one of the most fascinating questions approached by neuroscience today. C. elegans provides a good model system for the investigation of neuronal networks, due to its compact nervous system and rather easy access to genetic manipulation. Most physical connections between neurons have been characterized using EM reconstruction, a big step towards an extensive elucidation of the functional connections between these neurons, e.g. by mutant studies, electrophysiology or calcium imaging, and linking them to the animals. behavior. Here we want to combine the method of calcium imaging with activity-regulating light-activated ion channels. This should provide a basic and fast method in order to facilitate an easy and widespread investigation of neuronal networks, which ideally can also be correlated to behavior. Depolarizing or hyperpolarizing neurons with light-sensitive proteins, namely channelrhodopsin or halorhodopsin, and expressing genetically encoded Ca2+ sensors (GECIs) like G-CaMPs or cameleons postsynaptically to monitor the resulting effect on neuronal activity, could be the easiest and minimally invasive way towards this. Here, different approaches in spatial and spectral separation are presented, to overcome the major limitation in combining these tools, i.e. the overlapping excitation spectra. The challenge of specific expression also is addressed within our group (see posters by Christian Schultheis and Cornelia Schmitt). To be able to test our systems in terms of functionality and to have a behavioral readout as a control, we are currently applying our techniques on testing paradigms like mini-networks consisting of just two neurons.

John Reece-Hoyes et al. (2006) European Worm Meeting "wTF2.0: A Fundamental First Step for Mapping the Caenorhabditis elegans Transcription Factor Localizome"

Marc Vidal, Denis Dupuy, John Reece-Hoyes, Ian Hope, Jane Shingles, A.J. Marian Walhout, Bart Deplancke, Christian Grove

[European Worm Meeting, 2006]

John Reece-Hoyes1, Bart Deplancke2, Jane Shingles1, Christian Grove2, Denis Dupuy3, A.J. Marian Walhout2, Marc Vidal3 and Ian Hope1. The Localization of Expression Mapping Project (LEMP) aims to use cloned C.elegans promoter fragments to generate a genome-wide set of expression patterns termed the Localizome. The Promoterome currently contains promoter fragments of up to 2kb from about 6,500 of the approximately 20,000 identified genes in the C.elegans genome. Using the Multisite Gateway system these promoter fragments are re-cloned upstream of GFP within an unc-119 rescue vector and the resulting constructs used to transform unc-119 mutant nematodes by a modified ballistic DNA transfer technique. The current focus of the LEMP is on C.elegans transcription factor genes with the view that these expression pattern data will be essential for mapping transcription regulatory networks. While C.elegans gene models have undergone continuous refinement, the extant lists of predicted C.elegans transcription factors (collectively referred to as wTF1.0) were in need of updating. We have identified a compendium of 934 transcription factor genes (referred to as wTF2.0) by interrogating Wormbase version 140 for proteins with appropriate Gene Ontology (GO) terms and then manually removed false positives (369) and added false negatives (373). The results of various bioinformatic analyses using wTF2.0 as well as how the list can be used to investigate regulatory networks will be discussed. We expect wTF2.0 to be a dynamic resource due to regular updating of the C.elegans genome annotation as well as changes in the functional annotations of protein domains. wTF2.0 will be accessible to the scientific community via an online interface where input is possible. wTF2.0 provides a starting point to decipher the transcription regulatory networks that control metazoan development and function.