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The Multilayer Connectome of Caenorhabditis elegans

Barry Bentley, Robyn Branicky, Christopher L. Barnes and 5 more

PLOS Computational Biology · 2016 · CC BY

doi:10.1371/journal.pcbi.1005283

Abstract

Connectomics has focused primarily on the mapping of synaptic links in the brain; yet it is well established that extrasynaptic volume transmission, especially via monoamines and neuropeptides, is also critical to brain function and occurs primarily outside the synaptic connectome. We have mapped the putative monoamine connections, as well as a subset of neuropeptide connections, in C. elegans based on new and published gene expression data. The monoamine and neuropeptide networks exhibit distinct topological properties, with the monoamine network displaying a highly disassortative star-like structure with a rich-club of interconnected broadcasting hubs, and the neuropeptide network showing a more recurrent, highly clustered topology. Despite the low degree of overlap between the extrasynaptic (or wireless) and synaptic (or wired) connectomes, we find highly significant multilink motifs of interaction, pinpointing locations in the network where aminergic and neuropeptide signalling modulate synaptic activity. Thus, the C. elegans connectome can be mapped as a multiplex network with synaptic, gap junction, and neuromodulator layers representing alternative modes of interaction between neurons. This provides a new topological plan for understanding how aminergic and peptidergic modulation of behaviour is achieved by specific motifs and loci of integration between hard-wired synaptic or junctional circuits and extrasynaptic signals wirelessly broadcast from a small number of modulatory neurons.

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References 88

  1. 1.

    Bullmore E, Sporns O. Complex brain networks: graph theoretical analysis of structural and functional systems. Nature reviews Neuroscience. 2009;10(3):186–98. Epub 2009/02/05.

    Not in our library10.1038/nrn2575

  2. 2.

    White J, Southgate E, Thomson J, Brenner S. The structure of the nervous system of the nematode Caenorhabditis elegans Phil Trans R Soc Lond (Biol). 1986;314:1–340.

    Not in our library10.1098/rstb.1986.0056

  3. 3.

    Albertson DG, Thomson JN. The pharynx of Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci. 1976;275:299–325.

    Not in our library10.1098/rstb.1976.0085

  4. 4.
  5. 5.
  6. 6.

    Watts DJ, Strogatz SH. Collective dynamics of 'small-world' networks. Nature. 1998;393(6684):440–2. Epub 1998/06/12.

    Not in our library10.1038/30918

  7. 7.
  8. 8.

    Barabasi AL, Albert R. Emergence of scaling in random networks. Science. 1999;286(5439):509–12. Epub 1999/10/16.

    Not in our library10.1126/science.286.5439.509

  9. 9.

    Bullmore E, Sporns O. The economy of brain network organization. Nature reviews Neuroscience. 2012;13(5):336–49. Epub 2012/04/14.

    Not in our library10.1038/nrn3214

  10. 10.
  11. 11.

    Towlson EK, Vertes PE, Ahnert SE, Schafer WR, Bullmore ET. The rich club of the C. elegans neuronal connectome. The Journal of neuroscience: the official journal of the Society for Neuroscience. 2013;33(15):6380–7. Epub 2013/04/12.

    Not in our library10.1523/jneurosci.3784-12.2013

  12. 12.

    Bargmann CI. Beyond the connectome: how neuromodulators shape neural circuits. BioEssays: news and reviews in molecular, cellular and developmental biology. 2012;34(6):458–65. Epub 2012/03/08.

    Not in our library10.1002/bies.201100185

  13. 13.

    Marder E. Neuromodulation of neuronal circuits: back to the future. Neuron. 2012;76(1):1–11. Epub 2012/10/09. PubMed Central PMCID: PMC3482119.

    Not in our library10.1016/j.neuron.2012.09.010

  14. 14.

    Brezina V. Beyond the wiring diagram: signalling through complex neuromodulator networks. Philosophical transactions of the Royal Society of London Series B, Biological sciences. 2010;365(1551):2363–74. Epub 2010/07/07. PubMed Central PMCID: PMC2894954.

    Not in our library10.1098/rstb.2010.0105

  15. 15.

    Walker RJ, Brooks HL, Holden-Dye L. Evolution and overview of classical transmitter molecules and their receptors. Parasitology. 1996;113 Suppl:S3–33. Epub 1996/01/01.

    Not in our library10.1017/s0031182000077878

  16. 16.

    Chase DL, Koelle MR. Biogenic amine neurotransmitters in C. elegans. WormBook: the online review of C elegans biology. 2007:1–15. Epub 2007/12/01.

    Not in our library10.1895/wormbook.1.132.1

  17. 17.

    Lin Z, Canales JJ, Bjorgvinsson T, Thomsen M, Qu H, Liu QR, et al Monoamine transporters: vulnerable and vital doorkeepers. Prog Mol Biol Transl Sci. 2011;98:1–46. Epub 2011/01/05. 21199769; PubMed Central PMCID: PMC3321928.

    Not in our library10.1016/b978-0-12-385506-0.00001-6

  18. 18.

    Li C, Kim K. Neuropeptides. WormBook: the online review of C elegans biology. 2008:1–36. Epub 2008/09/27. PubMed Central PMCID: PMC2749236.

    Not in our library10.1895/wormbook.1.142.1

  19. 19.

    Hobert O. The neuronal genome of Caenorhabditis elegans. WormBook: the online review of C elegans biology. 2013:1–106. Epub 2013/10/02.

    Not in our library10.1895/wormbook.1.161.1

  20. 20.

    Ringstad N, Abe N, Horvitz HR. Ligand-gated chloride channels are receptors for biogenic amines in C. elegans. Science. 2009;325(5936):96–100. Epub 2009/07/04. PubMed Central PMCID: PMC2963310.

    Not in our library10.1126/science.1169243

  21. 21.

    Chase DL, Koelle MR. Genetic analysis of RGS protein function in Caenorhabditis elegans. Methods in enzymology. 2004;389:305–20. Epub 2004/08/18.

    Not in our library10.1016/s0076-6879(04)89018-9

  22. 22.

    Gurel G, Gustafson MA, Pepper JS, Horvitz HR, Koelle MR. Receptors and other signaling proteins required for serotonin control of locomotion in Caenorhabditis elegans. Genetics. 2012;192(4):1359–71. Epub 2012/10/02. PubMed Central PMCID: PMC3512144.

    Not in our library10.1534/genetics.112.142125

  23. 23.

    Jafari G, Xie Y, Kullyev A, Liang B, Sze JY. Regulation of extrasynaptic 5-HT by serotonin reuptake transporter function in 5-HT-absorbing neurons underscores adaptation behavior in Caenorhabditis elegans. The Journal of neuroscience: the official journal of the Society for Neuroscience. 2011;31(24):8948–57. Epub 2011/06/17. PubMed Central PMCID: PMC3153855.

    Not in our library10.1523/jneurosci.1692-11.2011

  24. 24.

    Duerr JS, Frisby DL, Gaskin J, Duke A, Asermely K, Huddleston D, et al The cat-1 gene of Caenorhabditis elegans encodes a vesicular monoamine transporter required for specific monoamine-dependent behaviors. J Neurosci. 1999;19:72–84.

    Not in our library10.1523/jneurosci.19-01-00072.1999

  25. 25.

    Pocock R, Hobert O. Hypoxia activates a latent circuit for processing gustatory information in C. elegans. Nature neuroscience. 2010;13(5):610–4. Epub 2010/04/20. PubMed Central PMCID: PMC3733994.

    Not in our library10.1038/nn.2537

  26. 26.

    Nicosia V, Latora V. Measuring and modeling correlations in multiplex networks. Physical review E, Statistical, nonlinear, and soft matter physics. 2015;92(3):032805 Epub 2015/10/16.

    Not in our library10.1103/physreve.92.032805

  27. 27.

    Ezcurra M, Tanizawa Y, Swoboda P, Schafer WR. Food sensitizes C. elegans avoidance behaviours through acute dopamine signalling. The EMBO journal. 2011;30(6):1110–22. Epub 2011/02/10. PubMed Central PMCID: PMC3061029.

    Not in our library10.1038/emboj.2011.22

  28. 28.

    De Domenico M, Nicosia V, Arenas A, Latora V. Structural reducibility of multilayer networks. Nature communications. 2015;6:6864 Epub 2015/04/24.

    Not in our library10.1038/ncomms7864

  29. 29.

    Sorrentino F, di Bernardo M, Cuellar GH, Boccaletti S. Synchronization in weighted scale-free networks with degree-degree correlation. Physica D-Nonlinear Phenomena. 2006;224(1–2):123–9.

    Not in our library

  30. 30.
  31. 31.

    Wang S, Szalay MS, Zhang C, Csermely P. Learning and innovative elements of strategy adoption rules expand cooperative network topologies. PloS one. 2008;3(4):e1917 Epub 2008/04/10. PubMed Central PMCID: PMC2275790.

    Not in our library10.1371/journal.pone.0001917

  32. 32.

    Newman ME. Modularity and community structure in networks. Proceedings of the National Academy of Sciences of the United States of America. 2006;103(23):8577–82. Epub 2006/05/26. PubMed Central PMCID: PMC1482622.

    Not in our library10.1073/pnas.0601602103

  33. 33.

    Sporns O. Network attributes for segregation and integration in the human brain. Current opinion in neurobiology. 2013;23(2):162–71. Epub 2013/01/09.

    Not in our library10.1016/j.conb.2012.11.015

  34. 34.

    Li Z, Li Y, Yi Y, Huang W, Yang S, Niu W, et al Dissecting a central flip-flop circuit that integrates contradictory sensory cues in C. elegans feeding regulation. Nature communications. 2012;3:776 Epub 2012/04/12.

    Not in our library10.1038/ncomms1780

  35. 35.

    Chase DL, Pepper JS, Koelle MR. Mechanism of extrasynaptic dopamine signaling in Caenorhabditis elegans. Nature neuroscience. 2004;7(10):1096–103. Epub 2004/09/21.

    Not in our library10.1038/nn1316

  36. 36.

    van den Heuvel MP, Sporns O. Rich-club organization of the human connectome. The Journal of neuroscience: the official journal of the Society for Neuroscience. 2011;31(44):15775–86. Epub 2011/11/04.

    Not in our library10.1523/jneurosci.3539-11.2011

  37. 37.
  38. 38.

    de Reus MA, van den Heuvel MP. Rich club organization and intermodule communication in the cat connectome. The Journal of neuroscience: the official journal of the Society for Neuroscience. 2013;33(32):12929–39. Epub 2013/08/09.

    Not in our library10.1523/jneurosci.1448-13.2013

  39. 39.

    Shih CT, Sporns O, Yuan SL, Su TS, Lin YJ, Chuang CC, et al Connectomics-based analysis of information flow in the Drosophila brain. Current biology: CB. 2015;25(10):1249–58. Epub 2015/04/14.

    Not in our library10.1016/j.cub.2015.03.021

  40. 40.

    Colizza V, Flammini A, Serrano MA, Vespignani A. Detecting rich-club ordering in complex networks. Nature Physics. 2006;2(2):110–5.

    Not in our library

  41. 41.
  42. 42.

    Piggott BJ, Liu J, Feng Z, Wescott SA, Xu XZ. The neural circuits and synaptic mechanisms underlying motor initiation in C. elegans. Cell. 2011;147(4):922–33. Epub 2011/11/15. PubMed Central PMCID: PMC3233480.

    Not in our library10.1016/j.cell.2011.08.053

  43. 43.

    Wragg RT, Hapiak V, Miller SB, Harris GP, Gray J, Komuniecki PR, et al Tyramine and octopamine independently inhibit serotonin-stimulated aversive behaviors in Caenorhabditis elegans through two novel amine receptors. The Journal of neuroscience: the official journal of the Society for Neuroscience. 2007;27(49):13402–12. Epub 2007/12/07.

    Not in our library10.1523/jneurosci.3495-07.2007

  44. 44.

    Mori I, Ohshima Y. Neural regulation of thermotaxis in Caenorhabditis elegans. Nature. 1995;376:344–8.

    Not in our library10.1038/376344a0

  45. 45.

    Tsalik EL, Niacaris T, Wenick AS, Pau K, Avery L, Hobert O. LIM homeobox gene-dependent expression of biogenic amine receptors in restricted regions of the C. elegans nervous system. Developmental biology. 2003;263(1):81–102. Epub 2003/10/22. PubMed Central PMCID: PMC4445141.

    Not in our library10.1016/s0012-1606(03)00447-0

  46. 46.

    Gray JM, Hill JJ, Bargmann CI. A circuit for navigation in Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America. 2005;102(9):3184–91.

    Not in our library10.1073/pnas.0409009101

  47. 47.

    Menichetti G, Remondini D, Panzarasa P, Mondragon RJ, Bianconi G. Weighted multiplex networks. PloS one. 2014;9(6):e97857 Epub 2014/06/07. PubMed Central PMCID: PMC4048161.

    Not in our library10.1371/journal.pone.0097857

  48. 48.

    Zhang Y, Lu H, Bargmann CI. Pathogenic bacteria induce aversive olfactory learning in Caenorhabditis elegans. Nature. 2005;438(7065):179–84. Epub 2005/11/11.

    Not in our library10.1038/nature04216

  49. 49.

    Pirri JK, McPherson AD, Donnelly JL, Francis MM, Alkema MJ. A tyramine-gated chloride channel coordinates distinct motor programs of a Caenorhabditis elegans escape response. Neuron. 2009;62(4):526–38. Epub 2009/05/30. PubMed Central PMCID: PMC2804440.

    Not in our library10.1016/j.neuron.2009.04.013

  50. 50.

    Bhattacharya R, Touroutine D, Barbagallo B, Climer J, Lambert CM, Clark CM, et al A conserved dopamine-cholecystokinin signaling pathway shapes context-dependent Caenorhabditis elegans behavior. PLoS genetics. 2014;10(8):e1004584 Epub 2014/08/29. PubMed Central PMCID: PMC4148232.

    Not in our library10.1371/journal.pgen.1004584

  51. 51.

    Macosko EZ, Pokala N, Feinberg EH, Chalasani SH, Butcher RA, Clardy J, et al A hub-and-spoke circuit drives pheromone attraction and social behaviour in C. elegans. Nature. 2009;458(7242):1171–5. Epub 2009/04/08. PubMed Central PMCID: PMC2760495.

    Not in our library10.1038/nature07886

  52. 52.

    Jang H, Kim K, Neal SJ, Macosko E, Kim D, Butcher RA, et al Neuromodulatory State and Sex Specify Alternative Behaviors through Antagonistic Synaptic Pathways in C. elegans. Neuron. 2012;75(4):585–92. Epub 2012/08/28.

    Not in our library10.1016/j.neuron.2012.06.034

  53. 53.

    Chklovskii DB, Vitaladevuni S, Scheffer LK. Semi-automated reconstruction of neural circuits using electron microscopy. Current opinion in neurobiology. 2010;20(5):667–75. Epub 2010/09/14.

    Not in our library10.1016/j.conb.2010.08.002

  54. 54.

    Trueta C, De-Miguel FF. Extrasynaptic exocytosis and its mechanisms: a source of molecules mediating volume transmission in the nervous system. Front Physiol. 2012;3:319 Epub 2012/09/13. PubMed Central PMCID: PMC3432928.

    Not in our library10.3389/fphys.2012.00319

  55. 55.

    De-Miguel FF, Fuxe K. Extrasynaptic neurotransmission as a way of modulating neuronal functions. Front Physiol. 2012;3:16 Epub 2012/03/01. PubMed Central PMCID: PMC3279940.

    Not in our library10.3389/fphys.2012.00016

  56. 56.

    Fuxe K, Borroto-Escuela DO, Romero-Fernandez W, Diaz-Cabiale Z, Rivera A, Ferraro L, et al Extrasynaptic neurotransmission in the modulation of brain function. Focus on the striatal neuronal-glial networks. Front Physiol. 2012;3:136 Epub 2012/06/08. PubMed Central PMCID: PMC3366473.

    Not in our library10.3389/fphys.2012.00136

  57. 57.

    Owald D, Waddell S. Olfactory learning skews mushroom body output pathways to steer behavioral choice in Drosophila. Current opinion in neurobiology. 2015;35:178–84. Epub 2015/10/27.

    Not in our library10.1016/j.conb.2015.10.002

  58. 58.

    Kivelä M, Arenas A, Barthelemy M, Gleeson JP, Moreno Y, Porter MA. Multilayer networks. Journal of Complex Networks. 2014.

    Not in our library

  59. 59.

    Kashtan N, Itzkovitz S, Milo R, Alon U. Topological generalizations of network motifs. Physical review E, Statistical, nonlinear, and soft matter physics. 2004;70(3 Pt 1):031909.

    Not in our library10.1103/physreve.70.031909

  60. 60.
  61. 61.

    Ezak MJ, Ferkey DM. The C. elegans D2-like dopamine receptor DOP-3 decreases behavioral sensitivity to the olfactory stimulus 1-octanol. PloS one. 2010;5(3):e9487 Epub 2010/03/09. PubMed Central PMCID: PMC2830454.

    Not in our library10.1371/journal.pone.0009487

  62. 62.

    Harris GP, Hapiak VM, Wragg RT, Miller SB, Hughes LJ, Hobson RJ, et al Three distinct amine receptors operating at different levels within the locomotory circuit are each essential for the serotonergic modulation of chemosensation in Caenorhabditis elegans. The Journal of neuroscience: the official journal of the Society for Neuroscience. 2009;29(5):1446–56. Epub 2009/02/06. PubMed Central PMCID: PMC3418693.

    Not in our library10.1523/jneurosci.4585-08.2009

  63. 63.

    Serrano-Saiz E, Poole RJ, Felton T, Zhang F, De La Cruz ED, Hobert O. Modular control of glutamatergic neuronal identity in C. elegans by distinct homeodomain proteins. Cell. 2013;155(3):659–73. Epub 2013/11/19. PubMed Central PMCID: PMC3855022.

    Not in our library10.1016/j.cell.2013.09.052

  64. 64.

    Tanaka D, Furusawa K, Kameyama K, Okamoto H, Doi M. Melatonin signaling regulates locomotion behavior and homeostatic states through distinct receptor pathways in Caenorhabditis elegans. Neuropharmacology. 2007;53(1):157–68. Epub 2007/06/19.

    Not in our library10.1016/j.neuropharm.2007.04.017

  65. 65.

    Sykova E, Nicholson C. Diffusion in brain extracellular space. Physiol Rev. 2008;88(4):1277–340. Epub 2008/10/17. PubMed Central PMCID: PMC2785730.

    Not in our library10.1152/physrev.00027.2007

  66. 66.

    Taber KH, Hurley RA. Volume transmission in the brain: beyond the synapse. The Journal of neuropsychiatry and clinical neurosciences. 2014;26(1):iv, 1–4. Epub 2014/02/12.

    Not in our library10.1176/appi.neuropsych.13110351

  67. 67.

    Chan JP, Staab TA, Wang H, Mazzasette C, Butte Z, Sieburth D. Extrasynaptic muscarinic acetylcholine receptors on neuronal cell bodies regulate presynaptic function in Caenorhabditis elegans. The Journal of neuroscience: the official journal of the Society for Neuroscience. 2013;33(35):14146–59. Epub 2013/08/30. PubMed Central PMCID: PMC3756759.

    Not in our library10.1523/jneurosci.1359-13.2013

  68. 68.

    Dittman JS, Kaplan JM. Behavioral impact of neurotransmitter-activated G-protein-coupled receptors: muscarinic and GABAB receptors regulate Caenorhabditis elegans locomotion. The Journal of neuroscience: the official journal of the Society for Neuroscience. 2008;28(28):7104–12. Epub 2008/07/11. PubMed Central PMCID: PMC2679701.

    Not in our library10.1523/jneurosci.0378-08.2008

  69. 69.

    Pierce SB, Costa M, Wisotzkey R, Devadhar S, Homburger SA, Buchman AR, et al Regulation of DAF-2 receptor signaling by human insulin and ins-1, a member of the unusually large and diverse C. elegans insulin gene family. Genes & development. 2001;15(6):672–86. Epub 2001/03/29. PubMed Central PMCID: PMC312654.

    Not in our library10.1101/gad.867301

  70. 70.

    Chen BL, Hall DH, Chklovskii DB. Wiring optimization can relate neuronal structure and function. Proceedings of the National Academy of Sciences of the United States of America. 2006;103(12):4723–8.

    Not in our library10.1073/pnas.0506806103

  71. 71.

    Database of synaptic connectivity of C. elegans for computation [Internet]. 2003. Available from: http://ims.dse.ibaraki.ac.jp/ccep/index.html.

    Not in our library

  72. 72.

    WormAtlas [Internet]. 2002. Available from: http://www.wormatlas.org/.

    Not in our library

  73. 73.
  74. 74.

    WormWeb.org—C. elegans Interactive Neural Network. [Internet]. 2014 [cited 25 February 2016]. Available from: http://wormweb.org/neuralnet.

    Not in our library

  75. 75.

    Etchberger JF, Flowers EB, Poole RJ, Bashllari E, Hobert O. Cis-regulatory mechanisms of left/right asymmetric neuron-subtype specification in C. elegans. Development. 2009;136(1):147–60. Epub 2008/12/09. PubMed Central PMCID: PMC2685964.

    Not in our library10.1242/dev.030064

  76. 76.

    Newman MEJ. The structure and function of complex networks. SIAM Rev. 2003;45:167.

    Not in our library

  77. 77.

    Rubinov M, Sporns O. Complex network measures of brain connectivity: Uses and interpretations. Neuroimage. 2010;52(3):1059–69.

    Not in our library10.1016/j.neuroimage.2009.10.003

  78. 78.

    Wasserman S, Faust K. Social network analysis: methods and applications. Cambridge: Cambridge University Press; 1994 xxxi, 825 p. p.

    Not in our library

  79. 79.

    Leicht EA, Newman MEJ. Community structure in directed networks. Physical review letters. 2008;100(11). Artn 118703.

    Not in our library10.1103/physrevlett.100.118703

  80. 80.

    Newman MEJ. Assortative mixing in networks. Physical review letters. 2002;89(20). Artn 208701.

    Not in our library10.1103/physrevlett.89.208701

  81. 81.

    Ward JH. Hierarchical Grouping to Optimize an Objective Function. Journal of the American Statistical Association. 1963;58(301):236–44.

    Not in our library

  82. 82.

    Zhou S, Mondragon RJ. The rich-club phenomenon in the Internet topology. Ieee Communications Letters. 2004;8(3):180–2.

    Not in our library

  83. 83.

    Bianconi G. Statistical mechanics of multiplex networks: entropy and overlap. Physical review E, Statistical, nonlinear, and soft matter physics. 2013;87(6):062806 Epub 2013/07/16.

    Not in our library10.1103/physreve.87.062806

  84. 84.

    Boccaletti S, Bianconi G, Criado R, del Genio CI, Gomez-Gardenes J, Romance M, et al The structure and dynamics of multilayer networks. Physics Reports-Review Section of Physics Letters. 2014;544(1):1–122.

    Not in our library10.1016/j.physrep.2014.07.001

  85. 85.

    Bounova G, de Weck O. Overview of metrics and their correlation patterns for multiple- metric topology analysis on heterogeneous graph ensembles. Physical Review E. 2012;85(1). Artn 016117.

    Not in our library10.1103/physreve.85.016117

  86. 86.

    De Domenico M, Porter MA, Arenas A. MuxViz: a tool for multilayer analysis and visualization of networks. Journal of Complex Networks. 2015;3(2):159–76.

    Not in our library

  87. 87.

    Wernicke S, Rasche F. FANMOD: a tool for fast network motif detection. Bioinformatics. 2006;22(9):1152–3.

    Not in our library10.1093/bioinformatics/btl038

  88. 88.

    Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research. 2003;13(11):2498–504. Epub 2003/11/05. PubMed Central PMCID: PMC403769.

    Not in our library10.1101/gr.1239303

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