Publications

2024
Varun Sanjay Birari and Ithai Rabinowitch. 2024. “Asymmetry in synaptic connectivity balances redundancy and reachability in the Caenorhabditis elegans connectome.” iScience, 27, Pp. 110713. Publisher's Version Abstract

Summary

The brain is overall bilaterally symmetrical, but also exhibits considerable asymmetry. While symmetry may endow neural networks with robustness and resilience, asymmetry may enable parallel information processing and functional specialization. How is this tradeoff between symmetrical and asymmetrical brain architecture balanced? To address this, we focused on the Caenorhabditis elegans connectome, comprising 99 classes of bilaterally symmetrical neuron pairs. We found symmetry in the number of synaptic partners between neuron class members, but pronounced asymmetry in the identity of these synapses. We applied graph theoretical metrics for evaluating Redundancy, the selective reinforcement of specific neural paths by multiple alternative synaptic connections, and Reachability, the extent and diversity of synaptic connectivity of each neuron class. We found Redundancy and Reachability to be stochastically tunable by the level of network asymmetry, driving the C. elegans connectome to favor Redundancy over Reachability. These results elucidate fundamental relations between lateralized neural connectivity and function.

Michal Staum, Ayelet Chen Abraham, Reema Arbid, Varun Sanjay Birari, Matanel Dominitz, and Ithai Rabinowitch. 2024. “Behavioral adjustment of C. elegans to mechanosensory loss requires intact mechanosensory neurons.” PLOS Biology, 22, Pp. e3002729. Publisher's Version Abstract
Sensory neurons specialize in detecting and signaling the presence of diverse environmental stimuli. Neuronal injury or disease may undermine such signaling, diminishing the availability of crucial information. Can animals distinguish between a stimulus not being present and the inability to sense that stimulus in the first place? To address this question, we studied Caenorhabditis elegans nematode worms that lack gentle body touch sensation due to genetic mechanoreceptor dysfunction. We previously showed that worms can compensate for the loss of touch by enhancing their sense of smell, via an FLP-20 neuropeptide pathway. Here, we find that touch-deficient worms exhibit, in addition to sensory compensation, also cautious-like behavior, as if preemptively avoiding potential undetectable hazards. Intriguingly, these behavioral adjustments are abolished when the touch neurons are removed, suggesting that touch neurons are required for signaling the unavailability of touch information, in addition to their conventional role of signaling touch stimulation. Furthermore, we found that the ASE taste neurons, which similarly to the touch neurons, express the FLP-20 neuropeptide, exhibit altered FLP-20 expression levels in a touch-dependent manner, thus cooperating with the touch circuit. These results imply a novel form of neuronal signaling that enables C. elegans to distinguish between lack of touch stimulation and loss of touch sensation, producing adaptive behavioral adjustments that could overcome the inability to detect potential threats.
Netanel Cohen and Ithai Rabinowitch. 2024. “Resolving transitions between distinct phases of memory consolidation at high resolution in Caenorhabditis elegans.” iScience, 27, Pp. 111147. Publisher's Version Abstract

Summary

Memory consolidation following learning is a dynamic and complex process comprising several transitions between distinct memory phases. Although memory consolidation has been studied extensively, it remains difficult to draw an integral description that can delimit the transition points between specific memory phases at the behavioral, neuronal, and genetic levels. To this end, we have developed a rapid and robust aversive conditioning protocol for the nematode worm Caenorhabditis elegans, tracing memory consolidation within the first hour post conditioning and then up to 18 h post conditioning. This made it possible to uncover time-dependent involvement of primary sensory neurons, transcription and translation processes, and diverse gene populations in memory consolidation. The change in neuronal valence was strong enough to induce second order conditioning, and was amenable to considerable modulation in specific mutant strains. Together, our work lends memory consolidation to detailed temporal and spatial analysis, advancing system-wide understanding of learning and memory.

Ithai Rabinowitch, Daniel A. Colón-Ramos, and Michael Krieg. 2024. “Understanding neural circuit function through synaptic engineering.” Nature Reviews Neuroscience 2024 25:2, 25, Pp. 131-139. Publisher's Version Abstract
Synapses are a key component of neural circuits, facilitating rapid and specific signalling between neurons. Synaptic engineering — the synthetic insertion of new synaptic connections into in vivo neural circuits — is an emerging approach for neural circuit interrogation. This approach is especially powerful for establishing causality in neural circuit structure–function relationships, for emulating synaptic plasticity and for exploring novel patterns of circuit connectivity. Contrary to other approaches for neural circuit manipulation, synaptic engineering targets specific connections between neurons and functions autonomously with no user-controlled external activation. Synaptic engineering has been successfully implemented in several systems and in different forms, including electrical synapses constructed from ectopically expressed connexin gap junction proteins, synthetic optical synapses composed of presynaptic photon-emitting luciferase coupled with postsynaptic light-gated channels, and artificial neuropeptide signalling pathways. This Perspective describes these different methods and how they have been applied, and examines how the field may advance. Synaptic engineering involves the synthetic insertion of new synapses between neurons in vivo. In this Perspective, Rabinowitch, Colón-Ramos and Krieg explore this emerging approach for studying neural circuits, describing the different methods that have been used and how they have been implemented.
2022
Ithai Rabinowitch. 2022. “Inserting new synaptic connections into damaged neural circuits: Towards synapse therapy?.” Neural Regeneration Research, 17, 2, Pp. 300–301. Publisher's Version
2021
Ithai Rabinowitch, Bishal Upadhyaya, Aaradhya Pant, Dolev Galski, Lena Kreines, and Jihong Bai. 2021. “Circumventing Neural Damage in a C. elegans Chemosensory Circuit Using Genetically Engineered Synapses.” Cell Systems. Publisher's Version Abstract
Neuronal loss can considerably diminish neural circuit function, impairing normal behavior by disrupting information flow in the circuit. Here, we use genetically engineered electrical synapses to reroute the flow of information in a C. elegans damaged chemosensory circuit in order to restore organism behavior. We impaired chemotaxis by removing one pair of interneurons from the circuit then artificially coupled two other adjacent neuron pairs by ectopically expressing the gap junction protein, connexin, in them. This restored chemotaxis in the animals. We expected to observe linear and direct information flow between the connexin-coupled neurons in the recovered circuit but also revealed the formation of new potent left-right lateral electrical connections within the connexin-expressing neuron pairs. Our analysis suggests that these additional electrical synapses help restore circuit function by amplifying weakened neuronal signals in the damaged circuit in addition to emulating the wild-type circuit. A record of this paper's transparent peer review process is included in the Supplemental Information.
2020
Ithai Rabinowitch. 2020. “What would a synthetic connectome look like?.” Physics of Life Reviews, 33, Pp. 1-15. Publisher's Version Abstract
A major challenge of contemporary neuroscience is to unravel the structure of the connectome, the ensemble of neural connections that link between different functional units of the brain, and to reveal how this structure relates to brain function. This thriving area of research largely follows the general tradition in biology of reverse-engineering, which consists of first observing and characterizing a biological system or process, and then deconstructing it into its fundamental building blocks in order to infer its modes of operation. However, a complementary form of biology has emerged, synthetic biology, which emphasizes construction-based forward-engineering. The synthetic biology approach comprises the assembly of new biological systems out of elementary biological parts. The rationale is that the act of building a system can be a powerful method for gaining deep understanding of how that system works. As the fields of connectomics and synthetic biology are independently growing, I propose to consider the benefits of combining the two, to create synthetic connectomics, a new form of neuroscience and a new form of synthetic biology. The goal of synthetic connectomics would be to artificially design and construct the connectomes of live behaving organisms. Synthetic connectomics could serve as a unifying platform for unraveling the complexities of brain operation and perhaps also for generating new forms of artificial life, and, in general, could provide a valuable opportunity for empirically exploring theoretical predictions about network function. What would a synthetic connectome look like? What purposes would it serve? How could it be constructed? This review delineates the novel notion of a synthetic connectome and aims to lay out the initial steps towards its implementation, contemplating its impact on science and society.
Johanna Zech, Daniel Gold, Nadeen Salaymeh, Netanel Cohen Sasson, Ithai Rabinowitch, Jacob Golenser, and Karsten Mäder. 2020. “Oral Administration of Artemisone for the Treatment of Schistosomiasis: Formulation Challenges and In Vivo Efficacy.” Pharmaceutics, 12, 6, Pp. 509. Publisher's Version Abstract

Artemisone is an innovative artemisinin derivative with applications in the treatment of malaria, schistosomiasis and other diseases. However, its low aqueous solubility and tendency to degrade after solubilisation limits the translation of this drug into clinical practice. We developed a self-microemulsifying drug delivery system (SMEDDS), which is easy to produce (simple mixing) with a high drug load. In addition to known pharmaceutical excipients (Capmul MCM, Kolliphor HS15, propylene glycol), we identified Polysorb ID 46 as a beneficial new additional excipient. The physicochemical properties were characterized by dynamic light scattering, conductivity measurements, rheology and electron microscopy. High storage stability, even at 30 °C, was achieved. The orally administrated artemisone SMEDDS formulation was highly active in vivo in S. mansoni infected mice. Thorough elimination of the adult worms, their eggs and prevention of the deleterious granuloma formation in the livers of infected mice was observed even at a relatively low dose of the drug. The new formulation has a high potential to accelerate the clinical use of artemisone in schistosomiasis and malaria.

2019
Lisa Voelker, Bishal Upadhyaya, Denise M Ferkey, Sarah Woldemariam, Noelle D L'Etoile, Ithai Rabinowitch, and Jihong Bai. 2019. “INX-18 and INX-19 play distinct roles in electrical synapses that modulate aversive behavior in Caenorhabditis elegans.” PLoS Genet, 15, 10, Pp. e1008341. Abstract
In order to respond to changing environments and fluctuations in internal states, animals adjust their behavior through diverse neuromodulatory mechanisms. In this study we show that electrical synapses between the ASH primary quinine-detecting sensory neurons and the neighboring ASK neurons are required for modulating the aversive response to the bitter tastant quinine in C. elegans. Mutant worms that lack the electrical synapse proteins INX-18 and INX-19 become hypersensitive to dilute quinine. Cell-specific rescue experiments indicate that inx-18 operates in ASK while inx-19 is required in both ASK and ASH for proper quinine sensitivity. Imaging analyses find that INX-19 in ASK and ASH localizes to the same regions in the nerve ring, suggesting that both sides of ASK-ASH electrical synapses contain INX-19. While inx-18 and inx-19 mutant animals have a similar behavioral phenotype, several lines of evidence suggest the proteins encoded by these genes play different roles in modulating the aversive quinine response. First, INX-18 and INX-19 localize to different regions of the nerve ring, indicating that they are not present in the same synapses. Second, removing inx-18 disrupts the distribution of INX-19, while removing inx-19 does not alter INX-18 localization. Finally, by using a fluorescent cGMP reporter, we find that INX-18 and INX-19 have distinct roles in establishing cGMP levels in ASK and ASH. Together, these results demonstrate that electrical synapses containing INX-18 and INX-19 facilitate modulation of ASH nociceptive signaling. Our findings support the idea that a network of electrical synapses mediates cGMP exchange between neurons, enabling modulation of sensory responses and behavior.
Ithai Rabinowitch. 2019. “Synthetic biology in the brain: A vision of organic robots.” In Proceedings of the 2019 Conference on Artificial Life: How Can Artificial Life Help Solve Societal Challenges, ALIFE 2019, Pp. 654–655. Cambridge, MA: MIT Press. Publisher's Version Abstract
Synthetic biology lies on the interface between natural and artificial life. It consists of the assembly of natural biological components into artificially configured biological systems. A main focus of synthetic biology has been the engineering of new gene circuits that can produce artificial cellular functions. I propose to scale up this approach to include, beyond single cells and gene circuits, also entire multi-cellular organisms and the brain circuits that regulate their behavior. Such synthetic biology in the brain will offer new ways for understanding how brain connectivity relates to brain function, and could ultimately lead to futuristic technologies such as neuronally-programmed organic robots or biologically-based brain repair. As a first step towards this ambitious goal I have developed a technique for genetically inserting new synaptic connections into the nervous system of the nematode worm C. elegans, enabling the manipulation of information flow in the nervous system and the reprogramming of whole animal behavior in this organism. This approach may be expanded and adapted to other genetic models, and opens the way to possible new forms of artificial life. Such technology, if practiced responsibly, could offer considerable benefits to science, industry and medicine.
2018
Yee Lian Chew, Yoshinori Tanizawa, Yongmin Cho, Buyun Zhao, Alex J. Yu, Evan L. Ardiel, Ithai Rabinowitch, Jihong Bai, Catharine H. Rankin, Hang Lu, Isabel Beets, and William R. Schafer. 2018. “An Afferent Neuropeptide System Transmits Mechanosensory Signals Triggering Sensitization and Arousal in C. elegans.” Neuron, 99, 6, Pp. 1233–1246.e6. Publisher's Version Abstract
Summary Sensitization is a simple form of behavioral plasticity by which an initial stimulus, often signaling danger, leads to increased responsiveness to subsequent stimuli. Cross-modal sensitization is an important feature of arousal in many organisms, yet its molecular and neural mechanisms are incompletely understood. Here we show that in C. elegans, aversive mechanical stimuli lead to both enhanced locomotor activity and sensitization of aversive chemosensory pathways. Both locomotor arousal and cross-modal sensitization depend on the release of FLP-20 neuropeptides from primary mechanosensory neurons and on their receptor FRPR-3. Surprisingly, the critical site of action of FRPR-3 for both sensory and locomotor arousal is RID, a single neuroendocrine cell specialized for the release of neuropeptides that responds to mechanical stimuli in a FLP-20-dependent manner. Thus, FLP-20 peptides function as an afferent arousal signal that conveys mechanosensory information to central neurons that modulate arousal and other behavioral states.
2017
Bicheng Han, Yongming Dong, Lin Zhang, Yan Liu, Ithai Rabinowitch, and Jihong Bai. 2017. “Dopamine signaling tunes spatial pattern selectivity in C. elegans.” Elife, 6. Abstract
Animals with complex brains can discriminate the spatial arrangement of physical features in the environment. It is unknown whether such sensitivity to spatial patterns can be accomplished in simpler nervous that lack long-range sensory modalities such as vision and hearing. Here we show that the nematode can discriminate spatial patterns in its surroundings, despite having a nervous system of only 302 neurons. This spatial pattern selectivity requires touch-dependent dopamine signaling, including the mechanosensory TRP-4 channel in dopaminergic neurons and the D2-like dopamine receptor DOP-3. We find that spatial pattern selectivity varies significantly among wild isolates. Electrophysiological recordings show that natural variations in TRP-4 reduce the mechanosensitivity of dopaminergic neurons. Polymorphic substitutions in either TRP-4 or DOP-3 alter the selectivity of spatial patterns. Together, these results demonstrate an ancestral role for dopamine signaling in tuning spatial pattern preferences in a simple nervous system.
2016
Ithai Rabinowitch, Millet Treinin, and Jihong Bai. 2016. “Artificial Optogenetic TRN Stimulation of C. elegans.” Bio Protoc, 6, 20. Abstract
Optogenetics is a powerful tool for manipulating neuronal activity with high temporal and spatial precision. In the nematode C. elegans optogentics is especially useful and easy to apply. This is because C. elegans is translucent, so its neurons are highly accessible to optic stimulation. In addition, many of its neurons can be exclusively targeted using cell-specific promoters. We have recently taken advantage of optogentics to deliver artificial patterns of prolonged activation to a class of mechanosensory neurons, called touch receptor neurons (TRNs) in worms that lack touch sensation due to a genetic mutation. Our aim was to examine whether we can counteract the effects of sensory loss by artificially activating the sensory neurons. Here we describe in detail the various components of the protocol that we used. This consists of exposing worms expressing the light-sensitive ion channel Channelrohdopsin 2 (ChR2) in TRNs to long-term random flashes of light.
Ithai Rabinowitch and Jihong Bai. 2016. “The foundations of cross-modal plasticity.” Communicative and Integrative Biology, 9, 2, Pp. 1–3. Abstract
Cross-modal plasticity is a striking adaptive feature of the brain, whereby the loss of one sensory modality induces cortical reorganization that leads to enhanced sensory performance in remaining modalities. Much is known about the macroscopic modifications in the brain that underly cross-modal plasticity and the associated changes in sensory performance. In contrast there is relatively scant information about the molecular and cellular underpinnings of this mechanism. We hypothesized that cross-modal plasticity is a fundamental feature of the nervous system. As such, it should be found in organisms with brains that are substantially less complex than our own. Indeed, we discovered a cross-modal plasticity mechanism in the roundworm Caenorhabditis elegans, whose nervous system is composed of only 302 neurons. Taking advantage of the simplicity of the C. elegans nervous system, we were able to comprehensively study cross-modal plasticity from molecule through circuit to behavior.
Ithai Rabinowitch, Patrick Laurent, Buyun Zhao, Denise Walker, Isabel Beets, Liliane Schoofs, Jihong Bai, William R Schafer, and Millet Treinin. 2016. “Neuropeptide-Driven Cross-Modal Plasticity following Sensory Loss in Caenorhabditis elegans.” PLoS Biol, 14, 1, Pp. e1002348. Abstract
Sensory loss induces cross-modal plasticity, often resulting in altered performance in remaining sensory modalities. Whereas much is known about the macroscopic mechanisms underlying cross-modal plasticity, only scant information exists about its cellular and molecular underpinnings. We found that Caenorhabditis elegans nematodes deprived of a sense of body touch exhibit various changes in behavior, associated with other unimpaired senses. We focused on one such behavioral alteration, enhanced odor sensation, and sought to reveal the neuronal and molecular mechanisms that translate mechanosensory loss into improved olfactory acuity. To this end, we analyzed in mechanosensory mutants food-dependent locomotion patterns that are associated with olfactory responses and found changes that are consistent with enhanced olfaction. The altered locomotion could be reversed in adults by optogenetic stimulation of the touch receptor (mechanosensory) neurons. Furthermore, we revealed that the enhanced odor response is related to a strengthening of inhibitory AWC→AIY synaptic transmission in the olfactory circuit. Consistently, inserting in this circuit an engineered electrical synapse that diminishes AWC inhibition of AIY counteracted the locomotion changes in touch-deficient mutants. We found that this cross-modal signaling between the mechanosensory and olfactory circuits is mediated by neuropeptides, one of which we identified as FLP-20. Our results indicate that under normal function, ongoing touch receptor neuron activation evokes FLP-20 release, suppressing synaptic communication and thus dampening odor sensation. In contrast, in the absence of mechanosensory input, FLP-20 signaling is reduced, synaptic suppression is released, and this enables enhanced olfactory acuity; these changes are long lasting and do not represent ongoing modulation, as revealed by optogenetic experiments. Our work adds to a growing literature on the roles of neuropeptides in cross-modal signaling, by showing how activity-dependent neuropeptide signaling leads to specific cross-modal plastic changes in neural circuit connectivity, enhancing sensory performance.
2015
Ithai Rabinowitch and William R Schafer. 2015. “Engineering new synaptic connections in the C. elegans connectome..” Worm, 4, 2, Pp. e992668. Publisher's Version Abstract
Most of what we currently know about how neural circuits work we owe to methods based on the electrical or optical recording of neural activity. This is changing dramatically. First, the advent of optogenetic techinques has enabled precise manipulation of the activity of specific neurons. Second, the development of super-resolution methods for obtaining detailed maps of synaptic connectivity has paved the way for uncovering the connectomes of entire brains or brain regions. We describe a third and complementary new strategy for investigating and manipulating neural circuits: the artificial insertion of new synapses into existing neural circuits using genetic engineering tools. We have successfully accomplished this in C. elegans. Thus, In addition to being the first animal with an entirely mapped connectome, C. elegans is now also the first animal to have an editable connectome. Variations on this approach may be applicable in more complex nervous systems.
2014
Ithai Rabinowitch, Marios Chatzigeorgiou, Buyun Zhao, Millet Treinin, and William R. Schafer. 2014. “Rewiring neural circuits by the insertion of ectopic electrical synapses in transgenic C. elegans.” Nature Communications, 5. Publisher's Version Abstract
Neural circuits are functional ensembles of neurons that are selectively interconnected by chemical or electrical synapses. Here we describe a synthetic biology approach to the study of neural circuits, whereby new electrical synapses can be introduced in novel sites in the neuronal circuitry to reprogram behaviour. We added electrical synapses composed of the vertebrate gap junction protein Cx36 between Caenorhabditis elegans chemosensory neurons with opposite intrinsic responses to salt. Connecting these neurons by an ectopic electrical synapse led to a loss of lateral asymmetry and altered chemotaxis behaviour. In a second example, introducing Cx36 into an inhibitory chemical synapse between an olfactory receptor neuron and an interneuron changed the sign of the connection from negative to positive, and abolished the animal's behavioural response to benzaldehyde. These data demonstrate a synthetic strategy to rewire behavioural circuits by engineering synaptic connectivity in C. elegans.
2013
Ithai Rabinowitch, Marios Chatzigeorgiou, and William R. Schafer. 2013. “A gap junction circuit enhances processing of coincident mechanosensory inputs.” Current Biology, 23, 11, Pp. 963–967. Abstract
Electrical synapses have been shown to be important for enabling and detecting neuronal synchrony in both vertebrates [1-4] and invertebrates [5, 6]. Hub-and-spoke circuits, in which a central hub neuron is electrically coupled to several input neurons, are an overrepresented motif in the C. elegans nervous system [7] and may represent a conserved functional unit. The functional relevance of this configuration has been demonstrated for circuits mediating aggregation behavior [8] and nose touch perception [9]. Modeling approaches have been useful for understanding structurally and dynamically more complex electrical circuits [10, 11]. Therefore, we formulated a simple analytical model with minimal assumptions to obtain insight into the properties of the hub-and-spoke microcircuit motif. A key prediction of the model is that an active input neuron should facilitate activity throughout the network, whereas an inactive input should suppress network activity through shunting; this prediction was supported by cell ablation and in vivo neuroimaging experiments in the C. elegans nose touch circuit. Thus, the hub-and-spoke architecture may implement an analog coincidence detector enabling distinct responses to distributed and localized patterns of sensory input. ?? 2013 Elsevier Ltd.
2010
Juliette Ben Arous, Yoshinori Tanizawa, Ithai Rabinowitch, Didier Chatenay, and William R. Schafer. 2010. “Automated imaging of neuronal activity in freely behaving Caenorhabditis elegans.” Journal of Neuroscience Methods, 187, 2, Pp. 229–234. Abstract
In order to understand how neuronal circuits control locomotory patterns it is necessary to record neuronal activity of freely behaving animals. Here, using a new automated system for simultaneous recording of behavior and neuronal activity in freely moving Caenorhabditis elegans on standard agar plates, we show that spontaneous reversals from forward to backward locomotion reflect precisely the activity of the AVA command interneurons. We also witness spontaneous activity transients in the PLM sensory neurons during free behavior of the worm in standard conditions. We show that these activity transients are coupled to short spontaneous forward accelerations of the worm. © 2010 Elsevier B.V. All rights reserved.
2008
Ithai Rabinowitch and William R. Schafer. 2008. “Neuronal remodeling on the evolutionary timescale..” Journal of biology, 7, December, Pp. 37. Abstract
Despite its remarkable capacity to undergo change at timescales ranging from a fraction of a second to a lifetime, there are many aspects of the nervous system that can be modified only at the enormously longer evolutionary timescale. A new study in BMC Biology using nematodes illustrates such evolutionary neuronal remodeling.

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