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Avila B, Augusto P, Zimmer M, Serafino M, Makse HA. Fibration symmetries and cluster synchronization in the Caenorhabditis elegans connectome. ARXIV 2024:arXiv:2305.19367v2. [PMID: 37396607 PMCID: PMC10312817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Capturing how the Caenorhabditis elegans connectome structure gives rise to its neuron functionality remains unclear. It is through fiber symmetries found in its neuronal connectivity that synchronization of a group of neurons can be determined. To understand these we investigate graph symmetries and search for such in the symmetrized versions of the forward and backward locomotive sub-networks of the Caenorhabditi elegans worm neuron network. The use of ordinarily differential equations simulations admissible to these graphs are used to validate the predictions of these fiber symmetries and are compared to the more restrictive orbit symmetries. Additionally fibration symmetries are used to decompose these graphs into their fundamental building blocks which reveal units formed by nested loops or multilayered fibers. It is found that fiber symmetries of the connectome can accurately predict neuronal synchronization even under not idealized connectivity as long as the dynamics are within stable regimes of simulations.
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Affiliation(s)
- Bryant Avila
- Levich Institute, Physics Department, City College of New York, New York, NY, USA
| | - Pedro Augusto
- Vienna Biocenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Department of Neuroscience and Developmental Biology, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Manuel Zimmer
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
- Department of Neuroscience and Developmental Biology, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Matteo Serafino
- Levich Institute, Physics Department, City College of New York, New York, NY, USA
| | - Hernán A. Makse
- Levich Institute, Physics Department, City College of New York, New York, NY, USA
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Avila B, Serafino M, Augusto P, Zimmer M, Makse HA. Fibration symmetries and cluster synchronization in the Caenorhabditis elegans connectome. PLoS One 2024; 19:e0297669. [PMID: 38598455 PMCID: PMC11006206 DOI: 10.1371/journal.pone.0297669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 01/11/2024] [Indexed: 04/12/2024] Open
Abstract
Capturing how the Caenorhabditis elegans connectome structure gives rise to its neuron functionality remains unclear. It is through fiber symmetries found in its neuronal connectivity that synchronization of a group of neurons can be determined. To understand these we investigate graph symmetries and search for such in the symmetrized versions of the forward and backward locomotive sub-networks of the Caenorhabditi elegans worm neuron network. The use of ordinarily differential equations simulations admissible to these graphs are used to validate the predictions of these fiber symmetries and are compared to the more restrictive orbit symmetries. Additionally fibration symmetries are used to decompose these graphs into their fundamental building blocks which reveal units formed by nested loops or multilayered fibers. It is found that fiber symmetries of the connectome can accurately predict neuronal synchronization even under not idealized connectivity as long as the dynamics are within stable regimes of simulations.
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Affiliation(s)
- Bryant Avila
- Physics Department, Levich Institute, City College of New York, New York, NY, United Stated of America
| | - Matteo Serafino
- Physics Department, Levich Institute, City College of New York, New York, NY, United Stated of America
| | - Pedro Augusto
- Vienna Biocenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Department of Neuroscience and Developmental Biology, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Manuel Zimmer
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
- Department of Neuroscience and Developmental Biology, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Hernán A. Makse
- Physics Department, Levich Institute, City College of New York, New York, NY, United Stated of America
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3
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Lee TY, Yang W, Cha DS, Han YT. Synthesis of a natural quinoline alkaloid isolated from the deep-sea-derived fungus and its potential as a therapeutic for Parkinson's disease. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2023; 25:446-455. [PMID: 35980025 DOI: 10.1080/10286020.2022.2104259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/17/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
2-(Quinoline-8-carboxamido)benzoic acid (2-QBA; 1) is a natural quinoline alkaloid isolated from the deep-sea-derived fungus Aspergillus sp. SCSIO06786. Alkaloid 1 was synthesized by an amidation reaction of 8-quinolinecaroxylic acid with methyl anthranilate, followed by hydrolysis. The neuroprotective properties of 1 were evaluated using a Caenorhabditis elegans Parkinson's disease model, which revealed that 1 significantly ameliorated 1-methyl-4-phenylpyridinium (MPP+)-induced dopaminergic neurodegeneration in a dose-dependent manner. MPP+-induced behavioral defects in worms, including impaired locomotion and basal slowing ability, were restored by treatment with 1. We further demonstrated that treatment with 1 modulates the formation of neurotoxic α-synuclein oligomers by suppressing α-synuclein expressions and enhancing proteasome activity. These results suggest that 1 is a promising therapeutic candidate for the treatment of Parkinson's disease.
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Affiliation(s)
- Tae Yeon Lee
- College of Pharmacy, Dankook University, Cheonan 31116, South Korea
| | - Wooin Yang
- College of Pharmacy, Woosuk University, Wanju-gun 55338, South Korea
| | - Dong Seok Cha
- College of Pharmacy, Woosuk University, Wanju-gun 55338, South Korea
| | - Young Taek Han
- College of Pharmacy, Dankook University, Cheonan 31116, South Korea
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Pechuk V, Goldman G, Salzberg Y, Chaubey AH, Bola RA, Hoffman JR, Endreson ML, Miller RM, Reger NJ, Portman DS, Ferkey DM, Schneidman E, Oren-Suissa M. Reprogramming the topology of the nociceptive circuit in C. elegans reshapes sexual behavior. Curr Biol 2022; 32:4372-4385.e7. [PMID: 36075218 DOI: 10.1016/j.cub.2022.08.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/28/2022] [Accepted: 08/15/2022] [Indexed: 10/14/2022]
Abstract
The effect of the detailed connectivity of a neural circuit on its function and the resulting behavior of the organism is a key question in many neural systems. Here, we study the circuit for nociception in C. elegans, which is composed of the same neurons in the two sexes that are wired differently. We show that the nociceptive sensory neurons respond similarly in the two sexes, yet the animals display sexually dimorphic behaviors to the same aversive stimuli. To uncover the role of the downstream network topology in shaping behavior, we learn and simulate network models that replicate the observed dimorphic behaviors and use them to predict simple network rewirings that would switch behavior between the sexes. We then show experimentally that these subtle synaptic rewirings indeed flip behavior. Interestingly, when presented with aversive cues, rewired males were compromised in finding mating partners, suggesting that network topologies that enable efficient avoidance of noxious cues have a reproductive "cost." Our results present a deconstruction of the design of a neural circuit that controls sexual behavior and how to reprogram it.
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Affiliation(s)
- Vladyslava Pechuk
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gal Goldman
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yehuda Salzberg
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aditi H Chaubey
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - R Aaron Bola
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Jonathon R Hoffman
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Morgan L Endreson
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Renee M Miller
- Department of Brain and Cognitive Sciences, University of Rochester, Rochester, NY 14627, USA
| | - Noah J Reger
- Department of Biomedical Genetics, University of Rochester, Rochester, NY 14642, USA
| | - Douglas S Portman
- Department of Biomedical Genetics, University of Rochester, Rochester, NY 14642, USA
| | - Denise M Ferkey
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Elad Schneidman
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Meital Oren-Suissa
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Naudin L, Jiménez Laredo JL, Liu Q, Corson N. Systematic generation of biophysically detailed models with generalization capability for non-spiking neurons. PLoS One 2022; 17:e0268380. [PMID: 35560186 PMCID: PMC9106219 DOI: 10.1371/journal.pone.0268380] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/28/2022] [Indexed: 11/18/2022] Open
Abstract
Unlike spiking neurons which compress continuous inputs into digital signals for transmitting information via action potentials, non-spiking neurons modulate analog signals through graded potential responses. Such neurons have been found in a large variety of nervous tissues in both vertebrate and invertebrate species, and have been proven to play a central role in neuronal information processing. If general and vast efforts have been made for many years to model spiking neurons using conductance-based models (CBMs), very few methods have been developed for non-spiking neurons. When a CBM is built to characterize the neuron behavior, it should be endowed with generalization capabilities (i.e. the ability to predict acceptable neuronal responses to different novel stimuli not used during the model’s building). Yet, since CBMs contain a large number of parameters, they may typically suffer from a lack of such a capability. In this paper, we propose a new systematic approach based on multi-objective optimization which builds general non-spiking models with generalization capabilities. The proposed approach only requires macroscopic experimental data from which all the model parameters are simultaneously determined without compromise. Such an approach is applied on three non-spiking neurons of the nematode Caenorhabditis elegans (C. elegans), a well-known model organism in neuroscience that predominantly transmits information through non-spiking signals. These three neurons, arbitrarily labeled by convention as RIM, AIY and AFD, represent, to date, the three possible forms of non-spiking neuronal responses of C. elegans.
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Affiliation(s)
- Loïs Naudin
- Department of Applied Mathematics, Normandie University, Le Havre, Normandie, France
- * E-mail:
| | | | - Qiang Liu
- Department of Neuroscience, City University of Hong Kong, Kowloon, Hong Kong, SAR, China
| | - Nathalie Corson
- Department of Applied Mathematics, Normandie University, Le Havre, Normandie, France
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Liu J, Lu W, Yuan Y, Xin K, Zhao P, Gu X, Raza A, Huo H, Li Z, Fang T. Fixed Point Attractor Theory Bridges Structure and Function in C. elegans Neuronal Network. Front Neurosci 2022; 16:808824. [PMID: 35546893 PMCID: PMC9085386 DOI: 10.3389/fnins.2022.808824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/30/2022] [Indexed: 11/27/2022] Open
Abstract
Understanding the structure–function relationship in a neuronal network is one of the major challenges in neuroscience research. Despite increasing researches at circuit connectivity and neural network structure, their structure-based biological interpretability remains unclear. Based on the attractor theory, here we develop an analytical framework that links neural circuit structures and their functions together through fixed point attractor in Caenorhabditis elegans. In this framework, we successfully established the structural condition for the emergence of multiple fixed points in C. elegans connectome. Then we construct a finite state machine to explain how functions related to bistable phenomena at the neural activity and behavioral levels are encoded. By applying the proposed framework to the command circuit in C. elegans, we provide a circuit level interpretation for the forward-reverse switching behaviors. Interestingly, network properties of the command circuit and first layer amphid interneuron circuit can also be inferred from their functions in this framework. Our research indicates the reliability of the fixed point attractor bridging circuit structure and functions, suggesting its potential applicability to more complex neuronal circuits in other species.
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Affiliation(s)
- Jian Liu
- Department of Automation, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of System Control and Information Processing, Ministry of Education, Shanghai, China
| | - Wenbo Lu
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Ye Yuan
- Department of Automation, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of System Control and Information Processing, Ministry of Education, Shanghai, China
| | - Kuankuan Xin
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Peng Zhao
- Department of Automation, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of System Control and Information Processing, Ministry of Education, Shanghai, China
| | - Xiao Gu
- Department of Automation, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of System Control and Information Processing, Ministry of Education, Shanghai, China
| | - Asif Raza
- Department of Automation, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of System Control and Information Processing, Ministry of Education, Shanghai, China
| | - Hong Huo
- Department of Automation, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of System Control and Information Processing, Ministry of Education, Shanghai, China
- *Correspondence: Hong Huo,
| | - Zhaoyu Li
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Zhaoyu Li,
| | - Tao Fang
- Department of Automation, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of System Control and Information Processing, Ministry of Education, Shanghai, China
- Tao Fang,
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Olivares E, Izquierdo EJ, Beer RD. A Neuromechanical Model of Multiple Network Rhythmic Pattern Generators for Forward Locomotion in C. elegans. Front Comput Neurosci 2021; 15:572339. [PMID: 33679357 PMCID: PMC7930337 DOI: 10.3389/fncom.2021.572339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 01/21/2021] [Indexed: 12/04/2022] Open
Abstract
Multiple mechanisms contribute to the generation, propagation, and coordination of the rhythmic patterns necessary for locomotion in Caenorhabditis elegans. Current experiments have focused on two possibilities: pacemaker neurons and stretch-receptor feedback. Here, we focus on whether it is possible that a chain of multiple network rhythmic pattern generators in the ventral nerve cord also contribute to locomotion. We use a simulation model to search for parameters of the anatomically constrained ventral nerve cord circuit that, when embodied and situated, can drive forward locomotion on agar, in the absence of pacemaker neurons or stretch-receptor feedback. Systematic exploration of the space of possible solutions reveals that there are multiple configurations that result in locomotion that is consistent with certain aspects of the kinematics of worm locomotion on agar. Analysis of the best solutions reveals that gap junctions between different classes of motorneurons in the ventral nerve cord can play key roles in coordinating the multiple rhythmic pattern generators.
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Affiliation(s)
- Erick Olivares
- Cognitive Science Program, Indiana University Bloomington, Bloomington, IN, United States
| | - Eduardo J. Izquierdo
- Cognitive Science Program, Indiana University Bloomington, Bloomington, IN, United States
- Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, United States
| | - Randall D. Beer
- Cognitive Science Program, Indiana University Bloomington, Bloomington, IN, United States
- Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, United States
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9
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Naudin L, Corson N, Aziz-Alaoui MA, Jiménez Laredo JL, Démare T. On the Modeling of the Three Types of Non-spiking Neurons of the Caenorhabditis elegans. Int J Neural Syst 2020; 31:2050063. [PMID: 33269660 DOI: 10.1142/s012906572050063x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The nematode Caenorhabditis elegans (C. elegans) is a well-known model organism in neuroscience. The relative simplicity of its nervous system, made up of few hundred neurons, shares some essential features with more sophisticated nervous systems, including the human one. If we are able to fully characterize the nervous system of this organism, we will be one step closer to understanding the mechanisms underlying the behavior of living things. Following a recently conducted electrophysiological survey on different C. elegans neurons, this paper aims at modeling the three non-spiking RIM, AIY and AFD neurons (arbitrarily named with three upper case letters by convention). To date, they represent the three possible forms of non-spiking neuronal responses of the C. elegans. To achieve this objective, we propose a conductance-based neuron model adapted to the electrophysiological features of each neuron. These features are based on current biological research and a series of in-silico experiments which use differential evolution to fit the model to experimental data. From the obtained results, we formulate a series of biological hypotheses regarding currents involved in the neuron dynamics. These models reproduce experimental data with a high degree of accuracy while being biologically consistent with state-of-the-art research.
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Affiliation(s)
- Loïs Naudin
- Normandie Univ, UNIHAVRE, LMAH, FR-CNRS-3335, ISCN, Le Havre 76600, France
| | - Nathalie Corson
- Normandie Univ, UNIHAVRE, LMAH, FR-CNRS-3335, ISCN, Le Havre 76600, France
| | - M A Aziz-Alaoui
- Normandie Univ, UNIHAVRE, LMAH, FR-CNRS-3335, ISCN, Le Havre 76600, France
| | | | - Thibaut Démare
- Normandie Univ, UNIHAVRE, LITIS, FR-CNRS-3638, ISCN, Le Havre 76600, France
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10
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Fenyves BG, Szilágyi GS, Vassy Z, Sőti C, Csermely P. Synaptic polarity and sign-balance prediction using gene expression data in the Caenorhabditis elegans chemical synapse neuronal connectome network. PLoS Comput Biol 2020; 16:e1007974. [PMID: 33347479 PMCID: PMC7785220 DOI: 10.1371/journal.pcbi.1007974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 01/05/2021] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Graph theoretical analyses of nervous systems usually omit the aspect of connection polarity, due to data insufficiency. The chemical synapse network of Caenorhabditis elegans is a well-reconstructed directed network, but the signs of its connections are yet to be elucidated. Here, we present the gene expression-based sign prediction of the ionotropic chemical synapse connectome of C. elegans (3,638 connections and 20,589 synapses total), incorporating available presynaptic neurotransmitter and postsynaptic receptor gene expression data for three major neurotransmitter systems. We made predictions for more than two-thirds of these chemical synapses and observed an excitatory-inhibitory (E:I) ratio close to 4:1 which was found similar to that observed in many real-world networks. Our open source tool (http://EleganSign.linkgroup.hu) is simple but efficient in predicting polarities by integrating neuronal connectome and gene expression data.
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Affiliation(s)
- Bánk G. Fenyves
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
- Department of Emergency Medicine, Semmelweis University, Budapest, Hungary
| | - Gábor S. Szilágyi
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Zsolt Vassy
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Csaba Sőti
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Peter Csermely
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
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Manalo RVM, Medina PMB. Caffeine reduces deficits in mechanosensation and locomotion induced by L-DOPA and protects dopaminergic neurons in a transgenic Caenorhabditis elegans model of Parkinson's disease. PHARMACEUTICAL BIOLOGY 2020; 58:721-731. [PMID: 32715838 PMCID: PMC7470077 DOI: 10.1080/13880209.2020.1791192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
CONTEXT L-DOPA is the first-line drug for Parkinson's disease (PD). However, chronic use can lead to dyskinesia. Caffeine, which is a known neuroprotectant, can potentially act as an adjunct to minimise adverse effects of L-DOPA. OBJECTIVES This study determined changes in terms of neurodegeneration, locomotion and mechanosensation in Caenorhabditis elegans (Rhabditidae) strain UA57 overexpressing tyrosine hydroxylase (CAT-2) when treated with caffeine, L-DOPA or their combinations. MATERIALS AND METHODS Neurodegeneration was monitored via fluorescence microscopy of GFP-tagged dopaminergic neurons in the head and tail regions of C. elegans (n = 20). Meanwhile, mechanosensation and locomotion under vehicle (0.1% DMSO), L-DOPA (60 mM), caffeine (10 mM) or 60 mM L-DOPA + 10 or 20 mM caffeine (60LC10 and 60LC20) treatments were scored for 3 days. RESULTS L-DOPA (60 mM) reduced CEP and ADE neurons by 4.3% on day 3, with a concomitant decrease in fluorescence by 44.6%. This correlated with reductions in gentle head (-35%) and nose touch (-40%) responses, but improved locomotion (20-75%) compared with vehicle alone. CEP and ADE neuron counts were preserved with caffeine (10 mM) or 60LC10 (98-100%), which correlated with improved mechanosensation (10-23%) and locomotion (18-76%). However, none of the treatments was able to preserve PDE neuron count, reducing the basal slowing response. Discussion and conclusions: Taken together, we show that caffeine can protect DAergic neurons and can reduce aberrant locomotion and loss of sensation when co-administered with L-DOPA, which can potentially impact PD treatment and warrants further investigation.
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Affiliation(s)
- Rafael Vincent M. Manalo
- Biological Models Laboratory, Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila, Philippines
| | - Paul Mark B. Medina
- Biological Models Laboratory, Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila, Philippines
- CONTACT Paul Mark B. Medina Biological Models Laboratory, Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila, Philippines
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12
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Wright EAP, Goltsev AV. Statistical analysis of unidirectional and reciprocal chemical connections in the C. elegans connectome. Eur J Neurosci 2020; 52:4525-4535. [PMID: 33022789 DOI: 10.1111/ejn.14988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 11/29/2022]
Abstract
We analyze unidirectional and reciprocally connected pairs of neurons in the chemical connectomes of the male and hermaphrodite Caenorhabditis elegans, using recently published data. Our analysis reveals that reciprocal connections provide communication between most neurons with chemical synapses, and comprise on average more synapses than both unidirectional connections and the entire connectome. We further reveal that the C. elegans connectome is wired so that afferent connections onto neurons with large numbers of presynaptic neighbors (in-degree) comprise an above-average number of synapses (synaptic multiplicity). Notably, the larger the in-degree of a neuron the larger the synaptic multiplicity of its afferent connections. Finally, we show that the male forms two times fewer reciprocal connections between sex-shared neurons than the hermaphrodite, but a large number of reciprocal connections with male-specific neurons. These observations provide evidence for Hebbian structural plasticity in the C. elegans.
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Affiliation(s)
- Edgar A P Wright
- Department of Physics & I3N, University of Aveiro, Aveiro, Portugal
| | - Alexander V Goltsev
- Department of Physics & I3N, University of Aveiro, Aveiro, Portugal.,A.F. Ioffe Physico-Technical Institute, St. Petersburg, Russia
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13
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Towlson EK, Barabási AL. Synthetic ablations in the C. elegans nervous system. Netw Neurosci 2020; 4:200-216. [PMID: 32166208 PMCID: PMC7055645 DOI: 10.1162/netn_a_00115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/12/2019] [Indexed: 01/03/2023] Open
Abstract
Synthetic lethality, the finding that the simultaneous knockout of two or more individually nonessential genes leads to cell or organism death, has offered a systematic framework to explore cellular function, and also offered therapeutic applications. Yet the concept lacks its parallel in neuroscience—a systematic knowledge base on the role of double or higher order ablations in the functioning of a neural system. Here, we use the framework of network control to systematically predict the effects of ablating neuron pairs and triplets on the gentle touch response. We find that surprisingly small sets of 58 pairs and 46 triplets can reduce muscle controllability in this context, and that these sets are localized in the nervous system in distinct groups. Further, they lead to highly specific experimentally testable predictions about mechanisms of loss of control, and which muscle cells are expected to experience this loss. “Synthetic lethality” in cell biology is an extreme example of the effects of higher order genetic interactions: The simultaneous knockout of two or more individually nonessential genes leads to cell death. We define a neural analog to this concept in relation to the locomotor response to gentle touch in C. elegans. Two or more neurons are synthetic essential if individually they are not required for this behavior, yet their combination is. We employ a network control approach to systematically assess all pairs and triplets of neurons by their effect on body wall muscle controllability, and find that only surprisingly small sets of neurons are synthetic essential. They are highly localized in the nervous system and predicted to affect control over specific sets of muscles.
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Affiliation(s)
- Emma K Towlson
- Network Science Institute and Department of Physics, Northeastern University, Boston, MA, USA
| | - Albert-László Barabási
- Network Science Institute and Department of Physics, Northeastern University, Boston, MA, USA
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14
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Magaletta ME, Perkins KJ, Deuchler CP, Pieczynski JN. The Kinesin-3 motor, KLP-4, mediates axonal organization and cholinergic signaling in Caenorhabditis elegans. FASEB Bioadv 2019; 1:450-460. [PMID: 32123843 PMCID: PMC6996341 DOI: 10.1096/fba.2019-00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022] Open
Abstract
Microtubule plus-end directed trafficking is dominated by kinesin motors, yet kinesins differ in terms of cargo identity, movement rate, and distance travelled. Functional diversity of kinesins is especially apparent in polarized neurons, where long distance trafficking is required for efficient signal transduction-behavioral response paradigms. The Kinesin-3 superfamily are expressed in neurons and are hypothesized to have significant roles in neuronal signal transduction due to their high processivity. Although much is known about Kinesin-3 motors mechanistically in vitro, there is little known about their mechanisms in vivo. Here, we analyzed KLP-4, the Caenorhabditis elegans homologue of human KIF13A and KIF13B. Like other Kinesin-3 superfamily motors, klp-4 is highly expressed in the ventral nerve cord command interneurons of the animal, suggesting it might have a role in controlling movement of the animal. We characterized an allele of klp-4 that contains are large indel in the cargo binding domain of the motor, however, the gene still appears to be expressed. Behavioral analysis demonstrated that klp-4 mutants have defects in locomotive signaling, but not the strikingly uncoordinated movements such as those found in unc-104/KIF1A mutants. Animals with this large deletion are hypersensitive to the acetylcholinesterase inhibitor aldicarb but are unaffected by exogenous serotonin. Interestingly, this large klp-4 indel does not affect gross neuronal development but does lead to aggregation and disorganization of RAB-3 at synapses. Taken together, these data suggest a role for KLP-4 in modulation of cholinergic signaling in vivo and shed light on possible in vivo mechanisms of Kinesin-3 motor regulation.
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Affiliation(s)
- Margaret E. Magaletta
- Department of BiologyRollins CollegeWinter ParkFlorida
- Program in Molecular Medicine, Diabetes Center of ExcellenceUniversity of Massachusetts Medical SchoolWorcesterMassachusetts
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15
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DiLoreto EM, Chute CD, Bryce S, Srinivasan J. Novel Technological Advances in Functional Connectomics in C. elegans. J Dev Biol 2019; 7:E8. [PMID: 31018525 PMCID: PMC6630759 DOI: 10.3390/jdb7020008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/08/2019] [Accepted: 02/13/2019] [Indexed: 12/11/2022] Open
Abstract
The complete structure and connectivity of the Caenorhabditis elegans nervous system ("mind of a worm") was first published in 1986, representing a critical milestone in the field of connectomics. The reconstruction of the nervous system (connectome) at the level of synapses provided a unique perspective of understanding how behavior can be coded within the nervous system. The following decades have seen the development of technologies that help understand how neural activity patterns are connected to behavior and modulated by sensory input. Investigations on the developmental origins of the connectome highlight the importance of role of neuronal cell lineages in the final connectivity matrix of the nervous system. Computational modeling of neuronal dynamics not only helps reconstruct the biophysical properties of individual neurons but also allows for subsequent reconstruction of whole-organism neuronal network models. Hence, combining experimental datasets with theoretical modeling of neurons generates a better understanding of organismal behavior. This review discusses some recent technological advances used to analyze and perturb whole-organism neuronal function along with developments in computational modeling, which allows for interrogation of both local and global neural circuits, leading to different behaviors. Combining these approaches will shed light into how neural networks process sensory information to generate the appropriate behavioral output, providing a complete understanding of the worm nervous system.
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Affiliation(s)
- Elizabeth M DiLoreto
- Biology and Biotechnology Department, Worcester Polytechnic Institute, Worcester, MA 01605, USA.
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16
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17
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Karbowski J. Deciphering neural circuits for Caenorhabditis elegans behavior by computations and perturbations to genome and connectome. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2018.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Gleeson P, Lung D, Grosu R, Hasani R, Larson SD. c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2017.0379. [PMID: 30201842 PMCID: PMC6158223 DOI: 10.1098/rstb.2017.0379] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 01/03/2023] Open
Abstract
The OpenWorm project has the ambitious goal of producing a highly detailed in silico model of the nematode Caenorhabditis elegans. A crucial part of this work will be a model of the nervous system encompassing all known cell types and connections. The appropriate level of biophysical detail required in the neuronal model to reproduce observed high-level behaviours in the worm has yet to be determined. For this reason, we have developed a framework, c302, that allows different instances of neuronal networks to be generated incorporating varying levels of anatomical and physiological detail, which can be investigated and refined independently or linked to other tools developed in the OpenWorm modelling toolchain. This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.
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Affiliation(s)
- Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - David Lung
- Cyber-Physical Systems, Technische Universität Wien, Vienna, Austria
| | - Radu Grosu
- Cyber-Physical Systems, Technische Universität Wien, Vienna, Austria
| | - Ramin Hasani
- Cyber-Physical Systems, Technische Universität Wien, Vienna, Austria
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Olivares EO, Izquierdo EJ, Beer RD. Potential role of a ventral nerve cord central pattern generator in forward and backward locomotion in Caenorhabditis elegans. Netw Neurosci 2018; 2:323-343. [PMID: 30294702 PMCID: PMC6145852 DOI: 10.1162/netn_a_00036] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/06/2017] [Indexed: 01/03/2023] Open
Abstract
C. elegans locomotes in an undulatory fashion, generating thrust by propagating dorsoventral bends along its body. Although central pattern generators (CPGs) are typically involved in animal locomotion, their presence in C. elegans has been questioned, mainly because there has been no evident circuit that supports intrinsic network oscillations. With a fully reconstructed connectome, the question of whether it is possible to have a CPG in the ventral nerve cord (VNC) of C. elegans can be answered through computational models. We modeled a repeating neural unit based on segmentation analysis of the connectome. We then used an evolutionary algorithm to determine the unknown physiological parameters of each neuron so as to match the features of the neural traces of the worm during forward and backward locomotion. We performed 1,000 evolutionary runs and consistently found configurations of the neural circuit that produced oscillations matching the main characteristic observed in experimental recordings. In addition to providing an existence proof for the possibility of a CPG in the VNC, we suggest a series of testable hypotheses about its operation. More generally, we show the feasibility and fruitfulness of a methodology to study behavior based on a connectome, in the absence of complete neurophysiological details.
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Affiliation(s)
- Erick O Olivares
- Cognitive Science Program, Indiana University, Bloomington, IN, USA
| | | | - Randall D Beer
- Cognitive Science Program, Indiana University, Bloomington, IN, USA
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20
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Mirzakhalili E, Epureanu BI, Gourgou E. A mathematical and computational model of the calcium dynamics in Caenorhabditis elegans ASH sensory neuron. PLoS One 2018; 13:e0201302. [PMID: 30048509 PMCID: PMC6062085 DOI: 10.1371/journal.pone.0201302] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/28/2018] [Indexed: 12/31/2022] Open
Abstract
We propose a mathematical and computational model that captures the stimulus-generated Ca2+ transients in the C. elegans ASH sensory neuron. The rationale is to develop a tool that will enable a cross-talk between modeling and experiments, using modeling results to guide targeted experimental efforts. The model is built based on biophysical events and molecular cascades known to unfold as part of neurons' Ca2+ homeostasis mechanism, as well as on Ca2+ signaling events. The state of ion channels is described by their probability of being activated or inactivated, and the remaining molecular states are based on biochemically defined kinetic equations or known biochemical motifs. We estimate the parameters of the model using experimental data of hyperosmotic stimulus-evoked Ca2+ transients detected with a FRET sensor in young and aged worms, unstressed and exposed to oxidative stress. We use a hybrid optimization method composed of a multi-objective genetic algorithm and nonlinear least-squares to estimate the model parameters. We first obtain the model parameters for young unstressed worms. Next, we use these values of the parameters as a starting point to identify the model parameters for stressed and aged worms. We show that the model, in combination with experimental data, corroborates literature results. In addition, we demonstrate that our model can be used to predict ASH response to complex combinations of stimulation pulses. The proposed model includes for the first time the ASH Ca2+ dynamics observed during both "on" and "off" responses. This mathematical and computational effort is the first to propose a dynamic model of the Ca2+ transients' mechanism in C. elegans neurons, based on biochemical pathways of the cell's Ca2+ homeostasis machinery. We believe that the proposed model can be used to further elucidate the Ca2+ dynamics of a key C. elegans neuron, to guide future experiments on C. elegans neurobiology, and to pave the way for the development of more mathematical models for neuronal Ca2+ dynamics.
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Affiliation(s)
- Ehsan Mirzakhalili
- Mechanical Engineering Department, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Bogdan I. Epureanu
- Mechanical Engineering Department, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Eleni Gourgou
- Mechanical Engineering Department, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, Division of Geriatrics, Medical School, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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21
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Arnatkevic̆iūtė A, Fulcher BD, Pocock R, Fornito A. Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome. PLoS Comput Biol 2018; 14:e1005989. [PMID: 29432412 PMCID: PMC5825174 DOI: 10.1371/journal.pcbi.1005989] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 02/23/2018] [Accepted: 01/19/2018] [Indexed: 11/18/2022] Open
Abstract
Studies of nervous system connectivity, in a wide variety of species and at different scales of resolution, have identified several highly conserved motifs of network organization. One such motif is a heterogeneous distribution of connectivity across neural elements, such that some elements act as highly connected and functionally important network hubs. These brain network hubs are also densely interconnected, forming a so-called rich club. Recent work in mouse has identified a distinctive transcriptional signature of neural hubs, characterized by tightly coupled expression of oxidative metabolism genes, with similar genes characterizing macroscale inter-modular hub regions of the human cortex. Here, we sought to determine whether hubs of the neuronal C. elegans connectome also show tightly coupled gene expression. Using open data on the chemical and electrical connectivity of 279 C. elegans neurons, and binary gene expression data for each neuron across 948 genes, we computed a correlated gene expression score for each pair of neurons, providing a measure of their gene expression similarity. We demonstrate that connections between hub neurons are the most similar in their gene expression while connections between nonhubs are the least similar. Genes with the greatest contribution to this effect are involved in glutamatergic and cholinergic signaling, and other communication processes. We further show that coupled expression between hub neurons cannot be explained by their neuronal subtype (i.e., sensory, motor, or interneuron), separation distance, chemically secreted neurotransmitter, birth time, pairwise lineage distance, or their topological module affiliation. Instead, this coupling is intrinsically linked to the identity of most hubs as command interneurons, a specific class of interneurons that regulates locomotion. Our results suggest that neural hubs may possess a distinctive transcriptional signature, preserved across scales and species, that is related to the involvement of hubs in regulating the higher-order behaviors of a given organism.
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Affiliation(s)
- Aurina Arnatkevic̆iūtė
- Brain and Mental Health Laboratory, Monash Institute of Cognitive and Clinical Neurosciences, School of Psychological Sciences, Monash University, Clayton, VIC, Australia
| | - Ben D. Fulcher
- Brain and Mental Health Laboratory, Monash Institute of Cognitive and Clinical Neurosciences, School of Psychological Sciences, Monash University, Clayton, VIC, Australia
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Alex Fornito
- Brain and Mental Health Laboratory, Monash Institute of Cognitive and Clinical Neurosciences, School of Psychological Sciences, Monash University, Clayton, VIC, Australia
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22
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Gao S, Guan SA, Fouad AD, Meng J, Kawano T, Huang YC, Li Y, Alcaire S, Hung W, Lu Y, Qi YB, Jin Y, Alkema M, Fang-Yen C, Zhen M. Excitatory motor neurons are local oscillators for backward locomotion. eLife 2018; 7:e29915. [PMID: 29360035 PMCID: PMC5780044 DOI: 10.7554/elife.29915] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/22/2017] [Indexed: 01/16/2023] Open
Abstract
Cell- or network-driven oscillators underlie motor rhythmicity. The identity of C. elegans oscillators remains unknown. Through cell ablation, electrophysiology, and calcium imaging, we show: (1) forward and backward locomotion is driven by different oscillators; (2) the cholinergic and excitatory A-class motor neurons exhibit intrinsic and oscillatory activity that is sufficient to drive backward locomotion in the absence of premotor interneurons; (3) the UNC-2 P/Q/N high-voltage-activated calcium current underlies A motor neuron's oscillation; (4) descending premotor interneurons AVA, via an evolutionarily conserved, mixed gap junction and chemical synapse configuration, exert state-dependent inhibition and potentiation of A motor neuron's intrinsic activity to regulate backward locomotion. Thus, motor neurons themselves derive rhythms, which are dually regulated by the descending interneurons to control the reversal motor state. These and previous findings exemplify compression: essential circuit properties are conserved but executed by fewer numbers and layers of neurons in a small locomotor network.
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Affiliation(s)
- Shangbang Gao
- Key Laboratory of Molecular Biophysics of the Ministry of EducationCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Sihui Asuka Guan
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
- Department of PhysiologyUniversity of TorontoTorontoCanada
| | - Anthony D Fouad
- Department of BioengineeringSchool of Engineering and Applied Science, University of PennsylvaniaPhiladelphiaUnited States
| | - Jun Meng
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
- Department of PhysiologyUniversity of TorontoTorontoCanada
| | - Taizo Kawano
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
| | - Yung-Chi Huang
- Department of NeurobiologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Yi Li
- Key Laboratory of Molecular Biophysics of the Ministry of EducationCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Salvador Alcaire
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
- Department of PhysiologyUniversity of TorontoTorontoCanada
| | - Wesley Hung
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
| | - Yangning Lu
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
- Department of PhysiologyUniversity of TorontoTorontoCanada
| | - Yingchuan Billy Qi
- Neurobiology Section, Division of Biological SciencesUniversity of CaliforniaSan DiegoUnited States
| | - Yishi Jin
- Neurobiology Section, Division of Biological SciencesUniversity of CaliforniaSan DiegoUnited States
| | - Mark Alkema
- Department of NeurobiologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Christopher Fang-Yen
- Department of BioengineeringSchool of Engineering and Applied Science, University of PennsylvaniaPhiladelphiaUnited States
- Department of NeuroscienceUniversity of PennsylvaniaPhiladelphiaUnited States
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
- Department of PhysiologyUniversity of TorontoTorontoCanada
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23
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Rakowski F, Karbowski J. Optimal synaptic signaling connectome for locomotory behavior in Caenorhabditis elegans: Design minimizing energy cost. PLoS Comput Biol 2017; 13:e1005834. [PMID: 29155814 PMCID: PMC5714387 DOI: 10.1371/journal.pcbi.1005834] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 12/04/2017] [Accepted: 10/19/2017] [Indexed: 11/18/2022] Open
Abstract
The detailed knowledge of C. elegans connectome for 3 decades has not contributed dramatically to our understanding of worm's behavior. One of main reasons for this situation has been the lack of data on the type of synaptic signaling between particular neurons in the worm's connectome. The aim of this study was to determine synaptic polarities for each connection in a small pre-motor circuit controlling locomotion. Even in this compact network of just 7 neurons the space of all possible patterns of connection types (excitation vs. inhibition) is huge. To deal effectively with this combinatorial problem we devised a novel and relatively fast technique based on genetic algorithms and large-scale parallel computations, which we combined with detailed neurophysiological modeling of interneuron dynamics and compared the theory to the available behavioral data. As a result of these massive computations, we found that the optimal connectivity pattern that matches the best locomotory data is the one in which all interneuron connections are inhibitory, even those terminating on motor neurons. This finding is consistent with recent experimental data on cholinergic signaling in C. elegans, and it suggests that the system controlling locomotion is designed to save metabolic energy. Moreover, this result provides a solid basis for a more realistic modeling of neural control in these worms, and our novel powerful computational technique can in principle be applied (possibly with some modifications) to other small-scale functional circuits in C. elegans.
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Affiliation(s)
- Franciszek Rakowski
- Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Warsaw, Poland
- Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Jan Karbowski
- Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Warsaw, Poland
- Institute of Applied Mathematics and Mechanics, Department of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
- * E-mail:
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24
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Kuramochi M, Doi M. A Computational Model Based on Multi-Regional Calcium Imaging Represents the Spatio-Temporal Dynamics in a Caenorhabditis elegans Sensory Neuron. PLoS One 2017; 12:e0168415. [PMID: 28072834 PMCID: PMC5224993 DOI: 10.1371/journal.pone.0168415] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/30/2016] [Indexed: 11/18/2022] Open
Abstract
Due to the huge number of neuronal cells in the brain and their complex circuit formation, computer simulation of neuronal activity is indispensable to understanding whole brain dynamics. Recently, various computational models have been developed based on whole-brain calcium imaging data. However, these analyses monitor only the activity of neuronal cell bodies and treat the cells as point unit. This point-neuron model is inexpensive in computational costs, but the model is unrealistically simplistic at representing intact neural activities in the brain. Here, we describe a novel three-unit Ordinary Differential Equation (ODE) model based on the neuronal responses derived from a Caenorhabditis elegans salt-sensing neuron. We recorded calcium responses in three regions of the ASER neuron using a simple downstep of NaCl concentration. Our simple ODE model generated from a single recording can adequately reproduce and predict the temporal responses of each part of the neuron to various types of NaCl concentration changes. Our strategy which combines a simple recording data and an ODE mathematical model may be extended to realistically understand whole brain dynamics by computational simulation.
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Affiliation(s)
- Masahiro Kuramochi
- Biomedical Research Institute, AIST, Ibaraki, Japan
- DAI-LAB, Biomedical Research Institute, AIST, Ibaraki, Japan
- Life Science and Bioengineering, Graduated School of Life and Environment Sciences, University of Tsukuba, Ibaraki, Japan
| | - Motomichi Doi
- Biomedical Research Institute, AIST, Ibaraki, Japan
- DAI-LAB, Biomedical Research Institute, AIST, Ibaraki, Japan
- Life Science and Bioengineering, Graduated School of Life and Environment Sciences, University of Tsukuba, Ibaraki, Japan
- * E-mail:
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25
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Li CW, Lo CC, Chen BS. Estimating Sensorimotor Mapping From Stimuli to Behaviors to Infer C. elegans Movements by Neural Transmission Ability Through Connectome Databases. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2016; 27:2229-2241. [PMID: 26415185 DOI: 10.1109/tnnls.2015.2475395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
One of the ultimate goals of computational neuroscience is to quantitatively connect between complex neural circuits and behaviors. In the past decades, the touch response circuit in Caenorhabditis elegans (C. elegans) has extensively been investigated in studies using genetically modified or laser-ablated worms. Synaptic connections, including chemical and electrical synapses, have been identified for most neurons in the C. elegans. However, we still do not know whether the empirically observed touch responses can be derived from connectome reconstructed from databases. To address this issue, we defined the transmission abilities (or levels) of neurons in a rate model in order to infer the behaviors of wild-type and ablated worms in response to posterior/nose/anterior touch stimuli. Our analysis showed that transmission abilities can be used to identify sensorimotor mapping from stimuli to movements and then to infer the C. elegans behaviors under simulations based on the perspective of decision-making, and provide useful information about how chemical and electronic synapses should be combined in the neural network movement analysis. This paper reveals an efficient tool that provided insights into the functions of complex neural circuits.
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26
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Petrushin A, Ferrara L, Blau A. The Si elegans project at the interface of experimental and computational Caenorhabditis elegans neurobiology and behavior. J Neural Eng 2016; 13:065001. [PMID: 27739402 DOI: 10.1088/1741-2560/13/6/065001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVE In light of recent progress in mapping neural function to behavior, we briefly and selectively review past and present endeavors to reveal and reconstruct nervous system function in Caenorhabditis elegans through simulation. APPROACH Rather than presenting an all-encompassing review on the mathematical modeling of C. elegans, this contribution collects snapshots of pathfinding key works and emerging technologies that recent single- and multi-center simulation initiatives are building on. We thereby point out a few general limitations and problems that these undertakings are faced with and discuss how these may be addressed and overcome. MAIN RESULTS Lessons learned from past and current computational approaches to deciphering and reconstructing information flow in the C. elegans nervous system corroborate the need of refining neural response models and linking them to intra- and extra-environmental interactions to better reflect and understand the actual biological, biochemical and biophysical events that lead to behavior. Together with single-center research efforts, the Si elegans and OpenWorm projects aim at providing the required, in some cases complementary tools for different hardware architectures to support advancement into this direction. SIGNIFICANCE Despite its seeming simplicity, the nervous system of the hermaphroditic nematode C. elegans with just 302 neurons gives rise to a rich behavioral repertoire. Besides controlling vital functions (feeding, defecation, reproduction), it encodes different stimuli-induced as well as autonomous locomotion modalities (crawling, swimming and jumping). For this dichotomy between system simplicity and behavioral complexity, C. elegans has challenged neurobiologists and computational scientists alike. Understanding the underlying mechanisms that lead to a context-modulated functionality of individual neurons would not only advance our knowledge on nervous system function and its failure in pathological states, but have directly exploitable benefits for robotics and the engineering of brain-mimetic computational architectures that are orthogonal to current von-Neumann-type machines.
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Affiliation(s)
- Alexey Petrushin
- Dept. of Neuroscience and Brain Technologies (NBT), Italian Institute of Technology (IIT), 16163 Genoa, Italy
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27
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Winter PB, Brielmann RM, Timkovich NP, Navarro HT, Teixeira-Castro A, Morimoto RI, Amaral LAN. A network approach to discerning the identities of C. elegans in a free moving population. Sci Rep 2016; 6:34859. [PMID: 27725712 PMCID: PMC5057085 DOI: 10.1038/srep34859] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 09/21/2016] [Indexed: 12/22/2022] Open
Abstract
The study of C. elegans has led to ground-breaking discoveries in gene-function, neuronal circuits, and physiological responses. Subtle behavioral phenotypes, however, are often difficult to measure reproducibly. We have developed an experimental and computational infrastructure to simultaneously record and analyze the physical characteristics, movement, and social behaviors of dozens of interacting free-moving nematodes. Our algorithm implements a directed acyclic network that reconstructs the complex behavioral trajectories generated by individual C. elegans in a free moving population by chaining hundreds to thousands of short tracks into long contiguous trails. This technique allows for the high-throughput quantification of behavioral characteristics that require long-term observation of individual animals. The graphical interface we developed will enable researchers to uncover, in a reproducible manner, subtle time-dependent behavioral phenotypes that will allow dissection of the molecular mechanisms that give rise to organism-level behavior.
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Affiliation(s)
- Peter B Winter
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Renee M Brielmann
- Department of Molecular Biosciences, Rice Institute for Biomedical Sciences, Northwestern University, Evanston, IL, USA
| | - Nicholas P Timkovich
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Helio T Navarro
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Andreia Teixeira-Castro
- Department of Molecular Biosciences, Rice Institute for Biomedical Sciences, Northwestern University, Evanston, IL, USA.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Sciences, Northwestern University, Evanston, IL, USA
| | - Luis A N Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA.,Northwestern Institute on Complex Systems and Data Science, Northwestern University, Evanston, IL, USA.,Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
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28
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Izquierdo EJ, Beer RD. The whole worm: brain-body-environment models of C. elegans. Curr Opin Neurobiol 2016; 40:23-30. [PMID: 27336738 DOI: 10.1016/j.conb.2016.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/26/2016] [Accepted: 06/02/2016] [Indexed: 12/20/2022]
Abstract
Brain, body and environment are in continuous dynamical interaction, and it is becoming increasingly clear that an animal's behavior must be understood as a product not only of its nervous system, but also of the ongoing feedback of this neural activity through the biomechanics of its body and the ecology of its environment. Modeling has an essential integrative role to play in such an understanding. But successful whole-animal modeling requires an animal for which detailed behavioral, biomechanical and neural information is available and a modeling methodology which can gracefully cope with the constantly changing balance of known and unknown biological constraints. Here we review recent progress on both optogenetic techniques for imaging and manipulating neural activity and neuromechanical modeling in the nematode worm Caenorhabditis elegans. This work demonstrates both the feasibility and challenges of whole-animal modeling.
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Affiliation(s)
- Eduardo J Izquierdo
- Cognitive Science Program, Program in Neuroscience, School of Informatics and Computing, Indiana University, United States
| | - Randall D Beer
- Cognitive Science Program, Program in Neuroscience, School of Informatics and Computing, Indiana University, United States.
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Roberts WM, Augustine SB, Lawton KJ, Lindsay TH, Thiele TR, Izquierdo EJ, Faumont S, Lindsay RA, Britton MC, Pokala N, Bargmann CI, Lockery SR. A stochastic neuronal model predicts random search behaviors at multiple spatial scales in C. elegans. eLife 2016; 5:12572. [PMID: 26824391 PMCID: PMC4798983 DOI: 10.7554/elife.12572] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/19/2016] [Indexed: 12/20/2022] Open
Abstract
Random search is a behavioral strategy used by organisms from bacteria to humans to locate food that is randomly distributed and undetectable at a distance. We investigated this behavior in the nematode Caenorhabditis elegans, an organism with a small, well-described nervous system. Here we formulate a mathematical model of random search abstracted from the C. elegans connectome and fit to a large-scale kinematic analysis of C. elegans behavior at submicron resolution. The model predicts behavioral effects of neuronal ablations and genetic perturbations, as well as unexpected aspects of wild type behavior. The predictive success of the model indicates that random search in C. elegans can be understood in terms of a neuronal flip-flop circuit involving reciprocal inhibition between two populations of stochastic neurons. Our findings establish a unified theoretical framework for understanding C. elegans locomotion and a testable neuronal model of random search that can be applied to other organisms. An animal’s ability to rapidly and efficiently locate new sources of food in its environment can mean the difference between life and death. As a result, animals have evolved foraging strategies that are adapted to the distribution and detectability of food sources. Organisms ranging from bacteria to humans use one such strategy, called random search, to locate food that cannot be detected at a distance and that is randomly distributed in their surroundings. The biological mechanisms that underpin random search are relatively well understood in single-cell organisms such as bacteria, but this information tells us little about the mechanisms that are used by animals, which use their nervous system to control their foraging behavior. Roberts et al. have now investigated the biological basis for random search behavior in a tiny roundworm called Caenorhabditis elegans. This worm forages for pockets of bacteria in decaying plant matter and has a simple and well-understood nervous system. Roberts et al. used information on how the cells in this worm’s nervous system connect together into so-called “neural circuits” to generate a mathematical model of random searching. The model revealed that the worm’s neural circuitry for random searching can be understood in terms of two groups of neuron-like components that switch randomly between “ON” and “OFF” states. While one group promotes forward movement, the other promotes backward movement, which is associated with a change in search direction. These two groups inhibit each other so that only one group usually is active at a given time. By adjusting this model to reproduce the behavioral records of real worms searching for food, Roberts et al. could predict the key neuronal connections involved. These predictions were then confirmed by taking electrical recordings from neurons. The model could also account for the unexpected behavioral effects that are seen when a neuron in one of these groups was destroyed or altered by a genetic mutation. These findings thus reveal a biological mechanism for random search behavior in worms that might operate in other animals as well. The findings might also provide future insight into the neural circuits involved in sleep and wakefulness in mammals, which is organized in a similar way.
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Affiliation(s)
- William M Roberts
- Institute of Neuroscience, University of Oregon, Eugene, United States
| | - Steven B Augustine
- School of Nursing, University of Pennsylvania, Philadelphia, United States
| | | | - Theodore H Lindsay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Tod R Thiele
- Department of Biological Sciences, University of Toronto, Toronto, Canada
| | | | - Serge Faumont
- Institute of Neuroscience, University of Oregon, Eugene, United States
| | - Rebecca A Lindsay
- Department of Ophthalmology, The Vision Center, Children's Hospital Los Angeles, Los Angeles, United States
| | | | - Navin Pokala
- Department of Life Sciences, New York Institute of Technology, Old Westbury, United States
| | - Cornelia I Bargmann
- Howard Hughes Medical Institute, Rockefeller University, New York, United States
| | - Shawn R Lockery
- Institute of Neuroscience, University of Oregon, Eugene, United States
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30
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Pereira L, Kratsios P, Serrano-Saiz E, Sheftel H, Mayo AE, Hall DH, White JG, LeBoeuf B, Garcia LR, Alon U, Hobert O. A cellular and regulatory map of the cholinergic nervous system of C. elegans. eLife 2015; 4. [PMID: 26705699 PMCID: PMC4769160 DOI: 10.7554/elife.12432] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/22/2015] [Indexed: 12/18/2022] Open
Abstract
Nervous system maps are of critical importance for understanding how nervous systems develop and function. We systematically map here all cholinergic neuron types in the male and hermaphrodite C. elegans nervous system. We find that acetylcholine (ACh) is the most broadly used neurotransmitter and we analyze its usage relative to other neurotransmitters within the context of the entire connectome and within specific network motifs embedded in the connectome. We reveal several dynamic aspects of cholinergic neurotransmitter identity, including a sexually dimorphic glutamatergic to cholinergic neurotransmitter switch in a sex-shared interneuron. An expression pattern analysis of ACh-gated anion channels furthermore suggests that ACh may also operate very broadly as an inhibitory neurotransmitter. As a first application of this comprehensive neurotransmitter map, we identify transcriptional regulatory mechanisms that control cholinergic neurotransmitter identity and cholinergic circuit assembly. DOI:http://dx.doi.org/10.7554/eLife.12432.001 To better understand the nervous system—the most complex of all the body’s organs—scientists have begun to painstakingly map its many features. These maps can then be used as a basis for understanding how the nervous system develops and works. Researchers have mapped the connections – called synapses – between all the nerve cells in the nervous system of a simple worm called Caenorhabditis elegans. Cells communicate by releasing chemicals called neurotransmitters across the synapses, but it is not fully known which types of neurotransmitters are released across each of the synapses in C. elegans. Now, Pereira et al. have mapped all worm nerve cells that use a neurotransmitter called acetylcholine by fluorescently marking proteins that synthesize and transport the neurotransmitter. This map revealed that 52 of the 118 types of nerve cells in the worm use acetylcholine, making it the most widely used neurotransmitter. This information was then combined with the findings of previous work that investigated which nerve cells release some other types of neurotransmitters. The combined data mean that it is now known which neurotransmitter is used for signaling by over 90% of the nerve cells in C. elegans. Using the map, Pereira et al. found that some neurons release different neurotransmitters in the different sexes of the worm. Additionally, the experiments revealed a set of proteins that cause the nerve cells to produce acetylcholine. Some of these proteins affect the fates of connected nerve cells. Overall, this information will allow scientists to more precisely manipulate specific cells or groups of cells in the worm nervous system to investigate how the nervous system develops and is regulated. DOI:http://dx.doi.org/10.7554/eLife.12432.002
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Affiliation(s)
- Laura Pereira
- Department of Biological Sciences, Columbia University, New York, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Paschalis Kratsios
- Department of Biological Sciences, Columbia University, New York, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Esther Serrano-Saiz
- Department of Biological Sciences, Columbia University, New York, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Hila Sheftel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Avi E Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - David H Hall
- Department of Neuroscience, Albert Einstein College of Medicine, New York, United States
| | - John G White
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Brigitte LeBoeuf
- Department of Biology, Texas A&M University, College Station, United States
| | - L Rene Garcia
- Department of Biology, Texas A&M University, College Station, United States.,Howard Hughes Medical Institute, Texas A&M University, College Station, United States
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, New York, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Howard Hughes Medical Institute, Columbia University, New York, United States
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31
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Zhen M, Samuel ADT. C. elegans locomotion: small circuits, complex functions. Curr Opin Neurobiol 2015; 33:117-26. [PMID: 25845627 DOI: 10.1016/j.conb.2015.03.009] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 03/18/2015] [Accepted: 03/18/2015] [Indexed: 12/20/2022]
Abstract
With 302 neurons in the adult Caenorhabditis elegans nervous system, it should be possible to build models of complex behaviors spanning sensory input to motor output. The logic of the motor circuit is an essential component of such models. Advances in physiological, anatomical, and neurogenetic analysis are revealing a surprisingly complex signaling network in the worm's small motor circuit. We are progressing towards a systems level dissection of the network of premotor interneurons, motor neurons, and muscle cells that move the animal forward and backward in its environment.
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Affiliation(s)
- Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada M5G 1X5; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8; Department of Physiology, University of Toronto, Toronto, ON, Canada M5S 1A8.
| | - Aravinthan D T Samuel
- Center for Brain Science, Department of Physics, Harvard University, Cambridge, MA 02138, United States.
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32
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Pohanka M. Inhibitors of acetylcholinesterase and butyrylcholinesterase meet immunity. Int J Mol Sci 2014; 15:9809-25. [PMID: 24893223 PMCID: PMC4100123 DOI: 10.3390/ijms15069809] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 03/06/2014] [Accepted: 03/11/2014] [Indexed: 12/22/2022] Open
Abstract
Acetylcholinesterase (AChE) inhibitors are widely used for the symptomatic treatment of Alzheimer’s disease and other dementias. More recent use is for myasthenia gravis. Many of these inhibitors interact with the second known cholinesterase, butyrylcholinesterase (BChE). Further, evidence shows that acetylcholine plays a role in suppression of cytokine release through a “cholinergic anti-inflammatory pathway” which raises questions about the role of these inhibitors in the immune system. This review covers research and discussion of the role of the inhibitors in modulating the immune response using as examples the commonly available drugs, donepezil, galantamine, huperzine, neostigmine and pyridostigmine. Major attention is given to the cholinergic anti-inflammatory pathway, a well-described link between the central nervous system and terminal effector cells in the immune system.
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Affiliation(s)
- Miroslav Pohanka
- Faculty of Military Health Sciences, University of Defence, Trebesska 1575, Hradec Kralove CZ-50001, Czech Republic.
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