Zaslaver, Alon et al. (2011) International Worm Meeting "Functional dynamics in the C. elegans sensory system."

Sternberg, Paul, Zaslaver, Alon, Yee, Lisa

[International Worm Meeting, 2011]

A major goal of systems neuroscience is to understand how the brain encodes the external world. Here we use C. elegans to study how a myriad of environmental signals are identified and integrated by its sensory system. We have constructed a comprehensive library of transgenic animals, where each line expresses the genetically-encoded calcium indicator GCaMP in a different individual sensory neuron. This library contains the vast majority (>80%) of the sensory system in the hermaphrodite. Using microfluidics, we measured neural activity from individual neurons as animals were subjected to various stimuli. These experiments reveal that the external world is intricately mapped onto the sensory neurons, where some neurons respond to a broad range of signals, while other neurons are activated by a narrow spectrum of signals. Response dynamics also varies among the different sensory neurons: Some neurons remain active for the duration of the stimulation, whereas other neurons oscillate or exhibit a single brief 'spike-like' response. We next studied the behavioral outcome following activation or inhibition of individual sensory neurons. We generated an additional library of transgenic animals where each animal expresses a light-activated channel (either Channelrhodopsin or Archaerhodopsin) in individual sensory neurons. Behavior analysis (e.g., locomotion) reveals that only a selected set of sensory neurons directly modulate locomotion. The nature of the modulation as well as the response time varied among the different sensory neurons. In summary, using a comprehensive library of optogenetically-encoded transgenic animals, we revealed key design features in the C. elegans sensory system. To our knowledge, this is the first functional dynamics study performed at the level of the entire sensory system of an animal.

Zaslaver, Alon et al. (2009) International Worm Meeting "Metazoan operons accelerate transcription and recovery rates."

Sternberg, Paul, Baugh, Ryan, Zaslaver, Alon

[International Worm Meeting, 2009]

Existing theories efficiently explain why operons are advantageous in prokaryotes, but their emergence in metazoans is still an enigma. We present a combination of genomic meta-analysis, experiment and theory to explain how operons could be adaptive during metazoan evolution. Focusing first on C. elegans, we show that operon genes, typically consisted of growth genes, are significantly up-regulated during recovery from multiple growth arrested states, and that this expression pattern is anti-correlated to the expression pattern of non-operon genes. In addition, we find that transcriptional resources are initially limited during arrest recovery, and that recovering worms are extremely sensitive to any additional limitation in transcriptional resources. By clustering growth genes into operons, fewer promoters compete for limited transcriptional machinery, effectively increasing the concentration of transcriptional resources and accelerating growth during recovery. A simple mathematical model of transcription dynamics reveals how a moderate increase in transcriptional resources can lead to a substantial enhancement in transcription rate and recovery. We find evidence for this design principle in different nematodes (e.g., Pristionchus pacificus and Brugia malayi) as well as in the chordate Ciona intestinalis. As recovery from a growth arrested state into a fast growing state is a physiological feature shared by many metazoans, operons could evolve as an evolutionary solution to facilitate these processes.

Itskovits, Eyal et al. (2015) International Worm Meeting "A new multi-worm tracker reveals unprecedented insights on worm chemotaxis."

Itskovits, Eyal, Zaslaver, Alon

[International Worm Meeting, 2015]

We have developed a novel Multi Worm Tracker (MWT) that is capable of tracking over a hundred worms simultaneously. The tracker employs a machine learning classification approach to identify the behaving worms. The system produces a long informative track for each individual worm, and generally maintains tracking despite frequent animal collision events. This MWT provides unprecedented statistical power revealing subtle, yet significant, behavioral features. Here we present results that challenge the prevalent "biased random walk" strategy of worms' chemotaxis. Moreover, we readily obtain data with satisfactory statistical significance following a single chemotaxis assay. Our system includes a suite of solutions for acquisition, tracking, and statistical analyses via a friendly user interface that is easy to operate with minimal programming skills.

Azulay, Aharon et al. (2015) International Worm Meeting "The common neighbor rule as an organizing principle in the C. elegans neural network."

Itskovic, Eyal, Zaslaver, Alon, Azulay, Aharon

[International Worm Meeting, 2015]

Background:A major goal of Systems Neuroscience is to decipher the structure-function relationship in neural networks. Recently, a new organizing principle-the Common Neighbor Rule-was found in the rat cortex. According to this rule, the more common neighbors a pair of neuron has, the more likely that this pair of neurons will be connected. Same principle is found in social networks (e.g. Facebook) where two individuals sharing multiple mutual friends are more likely to be friends as well. While the emergence of this principle in social networks may be intuitive, it is not clear why would this rule prevail in neural networks.Results:To address this question we studied the C. elegans neural network for which a fully-mapped wiring diagram of its 302 neurons is available. Strikingly, we find that the CNR is a prominent feature of the C. elegans connectome. Moreover, as common neighbor sets are made of neural triads, network analyses algorithms revealed highly homogeneous structures that consist of almost only one triad. Furthermore, these homogeneous sets are embedded in the network in defined functional layers; specifically, in a set consisted of mutually synapsing neurons, these two neurons will reside on the same layer while their common neighbors will be on a different layer. Such mutually-regulating and mutually-regulated structural blocks are enriched in the sensory- and motor-neurons, respectively, and can therefore serve as integration and synchronization devices. In addition, neurons connected in a Feed-forward fashion tend to reside on different layers of the network underscoring their role in signal propagation. Finally, coarse-graining the network based on the common neighbor sets revealed previously overlooked key functionalities of the network.Conclusion:These results can explain the emergence of the common neighbor rule as an organizing principle in neural networks.

Cho, Julie et al. (2011) International Worm Meeting "Sleep-dependent Changes in the C. elegans Neural Network."

Sternberg, Paul, Cho, Julie, Zaslaver, Alon

[International Worm Meeting, 2011]

*equal contribution Sleep is a physiological state essential for human and animal health. This state is behaviorally characterized by inactivity and a decreased arousal in response to external stimuli. Despite the fact that this conserved behavior has been studied across various mammalian and non-mammalian species, the modulation of the neural network that governs this quiescent state is largely unknown. C. elegans offers a uniquely tractable system to study sleep regulation on the neural-wide level. Here we use optogenetic techniques to probe the dynamics in individual circuits during sleep. We targeted each level of information processing from sensory neurons through interneurons and conversion of this information to coordinated behavior through the motor circuit and muscles. Using a genetically-encoded calcium indicator, we find that sensory response to external stimuli is dampened in the sleeping worm as compared to the wake worm. To elucidate activity of downstream components of the circuit, we expressed the light-activated channelrhodopsin in specific cells or tissues. Response was followed with behavioral assays. Targeted activation of individual sensory neurons in the sleeping worms caused a delayed response when compared to wake worms. However, targeted activation of interneurons or motor neurons did not result in a delayed response. Furthermore, targeted activation of body wall muscles did not awake the worms, although the muscles did contract. These results show that inhibition occurs only in a subset of the sensory-motor circuit and suggest that the sleep state reflects modulation of the top levels of the neural network spanning the sensory and inter-neurons. This study offers the first step toward network-wide analysis of the sleep state, where targeted activation of specific neural components is achieved, and may shed light on the essential components that regulate sleep in animals in general.

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.

Zuela Noam et al. (2014) Methods "Measuring the effects of high CO levels in Caenorhabditis elegans."

Friedman Nurit, Zuela Noam, Zaslaver Alon, Gruenbaum Yosef

[Methods, 2014]

Carbon dioxide (CO2) is an important molecule in cell metabolism. It is also a byproduct of many physiological processes. In humans, impaired lung function and lung diseases disrupt the body's ability to dispose of CO2 and elevate its levels in the body (hypercapnia). Animal models allow further understanding of how CO2 is sensed in the body and what are the physiological responses to high CO2 levels. This information can provide new strategies in the battle against the detrimental effects of CO2 accumulation in lung diseases. The nematode Caenorhabditis elegans provides us with such a model animal due to its natural ability to sense and navigate through varying concentrations of CO2, as well as the fact that it can be genetically manipulated with ease. Here we describe the different methods used to measure the effects elevated levels of CO2 have on the molecular sensing mechanism and physiology of C. elegans.

Sapir, Amir et al. (2009) Worm Breeder's Gazette "Studying mechanisms of bacteria-to-metazoans horizontal gene transfer"

Zaslaver, Alon, Sternberg, Paul, DeModena, John, Sapir, Amir

[Worm Breeder's Gazette, 2009]

Sapir, Amir et al. (2009) International Worm Meeting "Toward characterization of bacteria-to-nematodes HGT."

Sternberg, Paul, Sapir, Amir, Zaslaver, Alon, DeModena, John

[International Worm Meeting, 2009]

Horizontal gene transfer (HTG) is a fundamental process among unicellular organisms for acquiring new traits. Although initially thought to be extremely rare in metazoans, recent whole-genome sequencing projects reveal extensive gene transfer from prokaryotes to metazoans. This type of gene transfer is particularly relevant for symbiotic organisms that occupy new niches, where survival requires acquisition of new genes not previously present in the organism''s gene pool. For example, hemi-cellulose hydrolysis, induced by plant parasitic nematodes, is thought to have been acquired by the transfer of bacterial genes to the plant parasites'' bacteriovorous ancestors. In contrast to HGT between bacteria, the sequence of events leading to bacteria-to-nematodes HGT, as well as the molecular details of this process, remain elusive. So far, mechanistic studies of HGT in metazoans have been hindered by its rare occurrence, and the fact that symbiotic organisms are usually not suitable for long in-lab evolutionary studies. Our aim is to study HGT by combining the powerful genetics of E. coli (the donor) and C. elegans (the recipient). Specifically, we use the transfer of the unc-119 rescuing gene from E. coli to unc-119 mutant worms as an indicator for successful HGT. Rescued worms are examined to validate that gene transfer indeed happened, and these worms will be further analyzed to decipher the exact mechanism by which HGT occurred. We predict that the problem of identifying rare HGT events can be overcome by our experimental settings that involve growing multiple generations of worms in large numbers under specific selection. In a pilot experiment, we grew 4x106 worms per generation over 7 generations on E. coli carrying the unc-119 rescuing gene and validated that this approach is suitable for HGT studies. If HGT will not be identified, we will employ different conditions and genetic backgrounds that might increase HGT probabilities: i) Use of C. elegans mutants promoting bacterial propagation in the worm''s gut. ii) Exposing the cultured worms to various stress conditions. iii) Inducing HGT by unc-119 gene transposition in the E. coli donor. Ultimately, this system will serve as an empirical framework to elucidate the enigmatic process of bacteria-to-nematodes HGT.

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

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

[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.