Studying complex brain dynamics using Drosophila

References

• Aimon, S., Katsuki, T., Jia, T., Grosenick, L., Broxton, M., Deisseroth, K., … Greenspan, R.J. (2019a). Fast near-whole–brain imaging in adult Drosophila during responses to stimuli and behavior. PLOS Biology, 17, e2006732.
   PubMed Web of Science ®Google Scholar
• Aimon, S., Katsuki, T., Jia, T., Grosenick, L., Broxton, M., Deisseroth, K., …., Greenspan, R.J. (2019b). Whole-brain recordings of adult Drosophila using light field microscopy along with corresponding behavior or stimuli data. Dataset on CRCNS.Org.
   Google Scholar
• Aso, Y., Hattori, D., Yu, Y., Johnston, R.M., Iyer, N.A., Ngo, T.-T., … Rubin, G.M. (2014). The neuronal architecture of the mushroom body provides a logic for associative learning. ELife, 3, e04577. doi:10.7554/eLife.04577
   PubMed Web of Science ®Google Scholar
• Avena-Koenigsberger, A., Misic, B., & Sporns, O. (2018). Communication dynamics in complex brain networks. Nature Reviews Neuroscience, 19, 17–33. doi:10.1038/nrn.2017.149
   Web of Science ®Google Scholar
• Ayaz, A., Stäuble, A., Hamada, M., Wulf, M.-A., Saleem, A.B., & Helmchen, F. (2019). Layer-specific integration of locomotion and sensory information in mouse barrel cortex. Nature Communications, 10, 2585. doi:10.1038/s41467-019-10564-8
   PubMed Web of Science ®Google Scholar
• Bargmann, C.I., & Marder, E. (2013). From the connectome to brain function. Nature Methods, 10, 483–490. doi:10.1038/nmeth.2451
   PubMed Web of Science ®Google Scholar
• Bastos, A.M., & Schoffelen, J.-M. (2016). A tutorial review of functional connectivity analysis methods and their interpretational pitfalls. Frontiers in Systems Neuroscience, 9, 175. doi:10.3389/fnsys.2015.00175
   PubMed Web of Science ®Google Scholar
• Breakspear, M. (2017). Dynamic models of large-scale brain activity. Nature Neuroscience, 20, 340–352. doi:10.1038/nn.4497
   PubMed Web of Science ®Google Scholar
• Buzsáki, G. (2006). Rhythms of the brain. Oxford: Oxford University Press.
   Google Scholar
• Chen, C.-L., Hermans, L., Viswanathan, M.C., Fortun, D., Aymanns, F., Unser, M., … Ramdya, P. (2018). Imaging neural activity in the ventral nerve cord of behaving adult Drosophila. Nature Communications, 9, 4390. doi:10.1038/s41467-018-06857-z
   PubMed Web of Science ®Google Scholar
• Chen, T.-W., Wardill, T.J., Sun, Y., Pulver, S.R., Renninger, S.L., Baohan, A., … Kim, D.S. (2013). Ultrasensitive fluorescent proteins for imaging neuronal activity. Nature, 499, 295–300. doi:10.1038/nature12354
   PubMed Web of Science ®Google Scholar
• Costa, M., Manton, J.D., Ostrovsky, A.D., Prohaska, S., & Jefferis, G.S.X.E. (2016). NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases. Neuron, 91, 293–311. doi:10.1016/j.neuron.2016.06.012
   PubMed Web of Science ®Google Scholar
• Epskamp, S., & Fried, E.I. (2018). A tutorial on regularized partial correlation networks. Psychological Methods, 23, 617–634.
   PubMed Web of Science ®Google Scholar
• Franconville, R., Beron, C., & Jayaraman, V. (2018). Building a functional connectome of the Drosophila central complex. ELife, 7, e37017.
   PubMed Web of Science ®Google Scholar
• Green, J., Adachi, A., Shah, K.K., Hirokawa, J.D., Magani, P.S., & Maimon, G. (2017). A neural circuit architecture for angular integration in Drosophila. Nature, 546, 101–106. doi:10.1038/nature22343
   PubMed Web of Science ®Google Scholar
• Grosenick, L., Marshel, J.H., & Deisseroth, K. (2015). Closed-loop and activity-guided optogenetic control. Neuron, 86, 106–139. doi:10.1016/j.neuron.2015.03.034
   PubMed Web of Science ®Google Scholar
• Grover, D., Katsuki, T., & Greenspan, R.J. (2016). Flyception: imaging brain activity in freely walking fruit flies. Nature Methods, 13, 569–572. doi:10.1038/nmeth.3866
   PubMed Web of Science ®Google Scholar
• Grunwald Kadow, I.C. (2019). State-dependent plasticity of innate behavior in fruit flies. Current Opinion in Neurobiology, 54, 60–65. doi:10.1016/j.conb.2018.08.014
   PubMed Web of Science ®Google Scholar
• Holme, P., & Saramäki, J. (2012). Temporal networks. Physics Reports, 519, 97–125. doi:10.1016/j.physrep.2012.03.001
   Web of Science ®Google Scholar
• Huang, C., Maxey, J.R., Sinha, S., Savall, J., Gong, Y., & Schnitzer, M.J. (2018). Long-term optical brain imaging in live adult fruit flies. Nature Communications, 9, 872. doi:10.1038/s41467-018-02873-1
   PubMed Web of Science ®Google Scholar
• Ito, K., Shinomiya, K., Ito, M., Armstrong, J.D., Boyan, G., Hartenstein, V., … Vosshall, L.B. (2014). A systematic nomenclature for the insect brain. Neuron, 81, 755–765. doi:10.1016/j.neuron.2013.12.017
   PubMed Web of Science ®Google Scholar
• Ito, M., Masuda, N., Shinomiya, K., Endo, K., & Ito, K. (2013). Systematic analysis of neural projections reveals clonal composition of the Drosophila brain. Current Biology, 23, 644–655. doi:10.1016/j.cub.2013.03.015
   PubMed Web of Science ®Google Scholar
• Kass, R.E., Amari, S.-I., Arai, K., Brown, E.N., Diekman, C.O., Diesmann, M., … Kramer, M.A. (2018). Computational neuroscience: mathematical and statistical perspectives. Annual Review of Statistics and Its Application, 5, 183–214. doi:10.1146/annurev-statistics-041715-033733
   PubMed Web of Science ®Google Scholar
• Kim, S.M., Su, C.-Y., & Wang, J.W. (2017). Neuromodulation of innate behaviors in Drosophila. Annual Review of Neuroscience, 40, 327–348. doi:10.1146/annurev-neuro-072116-031558
   PubMed Web of Science ®Google Scholar
• Kim, S.S., Rouault, H., Druckmann, S., & Jayaraman, V. (2017). Ring attractor dynamics in the Drosophila central brain. Science, 356, 849–853. doi:10.1126/science.aal4835
   PubMed Web of Science ®Google Scholar
• Kohatsu, S., & Yamamoto, D. (2015). Visually induced initiation of Drosophila innate courtship-like following pursuit is mediated by central excitatory state. Nature Communications, 6, 6457. doi:10.1038/ncomms7457
   PubMed Web of Science ®Google Scholar
• Lemon, W.C., Pulver, S.R., Höckendorf, B., McDole, K., Branson, K., Freeman, J., & Keller, P.J. (2015). Whole-central nervous system functional imaging in larval Drosophila. Nature Communications, 6, 7924. doi:10.1038/ncomms8924
   PubMed Web of Science ®Google Scholar
• Li, W., Voleti, V., Schaffer, E., Vaadia, R., Grueber, W.B., Richard, S., & Hillman, E. (2016). SCAPE microscopy for high speed, 3D whole-brain imaging in Drosophila melanogaster. Paper presented at Biomedical Optics Congress, Fort Lauderdale, Florida United States, 2016, 4–6.
   Google Scholar
• Magrans de Abril, I., Yoshimoto, J., & Doya, K. (2018). Connectivity inference from neural recording data: Challenges, mathematical bases and research directions. Neural Networks, 102, 120–137. doi:10.1016/j.neunet.2018.02.016
   PubMed Web of Science ®Google Scholar
• Mann, K., Gallen, C.L., & Clandinin, T.R. (2017). Whole-brain calcium imaging reveals an intrinsic functional network in Drosophila. Current Biology, 27, 2389–2396.e4. doi:10.1016/j.cub.2017.06.076
   PubMed Web of Science ®Google Scholar
• Marder, E., & Taylor, A.L. (2011). Multiple models to capture the variability in biological neurons and networks. Nature Neuroscience, 14, 133–138. doi:10.1038/nn.2735
   PubMed Web of Science ®Google Scholar
• Nässel, D.R. (2002). Neuropeptides in the nervous system of Drosophila and other insects: multiple roles as neuromodulators and neurohormones. Progress in Neurobiology, 68, 1–84. doi:10.1016/S0301-0082(02)00057-6
   PubMed Web of Science ®Google Scholar
• Nichols, A.L.A., Eichler, T., Latham, R., & Zimmer, M. (2017). A global brain state underlies C. elegans sleep behavior. Science, 356, eaam6851. doi:10.1126/science.aam6851
   PubMed Web of Science ®Google Scholar
• O’Connell, R.G., Shadlen, M.N., Wong-Lin, K., & Kelly, S.P. (2018). Bridging neural and computational viewpoints on perceptual decision-making. Trends in Neurosciences, 41, 838–852. doi:10.1016/j.tins.2018.06.005
   PubMed Web of Science ®Google Scholar
• Pang, R., Lansdell, B.J., & Fairhall, A.L. (2016). Dimensionality reduction in neuroscience. Current Biology, 26, R656–R660. doi:10.1016/j.cub.2016.05.029
   PubMed Web of Science ®Google Scholar
• Panzera, L.C., & Hoppa, M.B. (2019). Genetically encoded voltage indicators are illuminating subcellular physiology of the axon. Frontiers in Cellular Neuroscience, 13, 52. doi:10.3389/fncel.2019.00052
   PubMed Web of Science ®Google Scholar
• Paulk, A.C., Kirszenblat, L., Zhou, Y., & van Swinderen, B. (2015). Closed-loop behavioral control increases coherence in the fly brain. Journal of Neuroscience, 35, 10304–10315. doi:10.1523/JNEUROSCI.0691-15.2015
   PubMed Web of Science ®Google Scholar
• Paulk, A.C., Zhou, Y., Stratton, P., Liu, L., & van Swinderen, B. (2013). Multichannel brain recordings in behaving Drosophila reveal oscillatory activity and local coherence in response to sensory stimulation and circuit activation. Journal of Neurophysiology, 110, 1703–1721. doi:10.1152/jn.00414.2013
   PubMed Web of Science ®Google Scholar
• Plaçais, P.-Y., de Tredern, É., Scheunemann, L., Trannoy, S., Goguel, V., Han, K.-A., … Preat, T. (2017). Upregulated energy metabolism in the Drosophila mushroom body is the trigger for long-term memory. Nature Communications, 8, 15510. doi:10.1038/ncomms15510
   PubMed Web of Science ®Google Scholar
• Plaçais, P.-Y., Trannoy, S., Isabel, G., Aso, Y., Siwanowicz, I., Belliart-Guérin, G., … Preat, T. (2012). Slow oscillations in two pairs of dopaminergic neurons gate long-term memory formation in Drosophila. Nature Neuroscience, 15, 592–599. doi:10.1038/nn.3055
   PubMed Web of Science ®Google Scholar
• Raccuglia, D., Huang, S., Ender, A., Heim, M.-M., Laber, D., Suárez-Grimalt, R., … Owald, D. (2019). Network-specific synchronization of electrical slow-wave oscillations regulates sleep drive in Drosophila. Current Biology, 29, 3611–3621.e3. In press. doi:10.1016/j.cub.2019.08.070
   PubMed Web of Science ®Google Scholar
• Russo, A.A., Bittner, S.R., Perkins, S.M., Seely, J.S., London, B.M., Lara, A.H., … Churchland, M.M. (2018). Motor cortex embeds muscle-like commands in an untangled population response. Neuron, 97, 953–966. doi:10.1016/j.neuron.2018.01.004
   PubMed Web of Science ®Google Scholar
• Schmidt, R., LaFleur, K.J.R., de Reus, M.A., van den Berg, L.H., & van den Heuvel, M.P. (2015). Kuramoto model simulation of neural hubs and dynamic synchrony in the human cerebral connectome. BMC Neuroscience, 16, 54. doi:10.1186/s12868-015-0193-z
   PubMed Web of Science ®Google Scholar
• Seeholzer, L.F., Seppo, M., Stern, D.L., & Ruta, V. (2018). Evolution of a central neural circuit underlies Drosophila mate preferences. Nature, 559, 564–569. doi:10.1038/s41586-018-0322-9
   PubMed Web of Science ®Google Scholar
• Seelig, J.D., & Jayaraman, V. (2015). Neural dynamics for landmark orientation and angular path integration. Nature, 521, 186–191. doi:10.1038/nature14446
   PubMed Web of Science ®Google Scholar
• Seelig, J.D., Chiappe, M.E., Lott, G.K., Dutta, A., Osborne, J.E., Reiser, M.B., & Jayaraman, V. (2010). Two-photon calcium imaging from head-fixed Drosophila during optomotor walking behavior. Nature Methods, 7, 535–540. doi:10.1038/nmeth.1468
   PubMed Web of Science ®Google Scholar
• Simpson, J.H., & Looger, L.L. (2018). Functional imaging and optogenetics in Drosophila. Genetics, 208, 1291–1309. doi:10.1534/genetics.117.300228
   PubMed Web of Science ®Google Scholar
• Sitaraman, D., Zars, M., LaFerriere, H., Chen, Y.-C., Sable-Smith, A., Kitamoto, T., … Zars, T. (2008). Serotonin is necessary for place memory in Drosophila. Proceedings of the National Academy of Sciences, 105, 5579–5584. doi:10.1073/pnas.0710168105
   PubMed Web of Science ®Google Scholar
• Stringer, C., Pachitariu, M., Steinmetz, N., Reddy, C.B., Carandini, M., & Harris, K.D. (2019). Spontaneous behaviors drive multidimensional, brainwide activity. Science, 364, eaav7893. doi:10.1126/science.aav7893
   Web of Science ®Google Scholar
• Strogatz, S.H. (2001). Nonlinear dynamics and chaos: With applications to physics, biology, chemistry, and engineering (1st ed.). Boulder, Colorado: Westview Press.
   Google Scholar
• Takens, F. (1981). Detecting strange attractors in turbulence. In: Rand D., Young L.S. (Eds.) Dynamical Systems and Turbulence, Warwick 1980. Lecture Notes in Mathematics. (Vol. 898) Berlin, Heidelberg: Springer.
   Google Scholar
• Tanaka, N.K., Ito, K., & Stopfer, M. (2009). Odor-evoked neural oscillations in Drosophila are mediated by widely branching interneurons. Journal of Neuroscience, 29, 8595–8603. doi:10.1523/JNEUROSCI.1455-09.2009
   PubMed Web of Science ®Google Scholar
• Tao, X., Lin, H.-H., Lam, T., Rodriguez, R., Wang, J.W., & Kubby, J. (2017). Transcutical imaging with cellular and subcellular resolution. Biomedical Optics Express, 8, 1277.
   PubMed Web of Science ®Google Scholar
• Vaadia, R.D., Li, W., Voleti, V., Singhania, A., Hillman, E.M.C., & Grueber, W.B. (2019). Characterization of proprioceptive system dynamics in behaving Drosophila larvae using high-speed volumetric microscopy. Current Biology, 29, 935–944.e4. doi:10.1016/j.cub.2019.01.060
   PubMed Web of Science ®Google Scholar
• Yap, M.H.W., Grabowska, M.J., Rohrscheib, C., Jeans, R., Troup, M., Paulk, A.C., … van Swinderen, B. (2017). Oscillatory brain activity in spontaneous and induced sleep stages in flies. Nature Communications, 8, 1815. doi:10.1038/s41467-017-02024-y
   PubMed Web of Science ®Google Scholar
• Zheng, Z., Lauritzen, J.S., Perlman, E., Robinson, C.G., Nichols, M., Milkie, D., … Bock, D.D. (2018). A complete electron microscopy volume of the brain of adult Drosophila melanogaster. Cell, 174, 730–743. doi:10.1016/j.cell.2018.06.019
   PubMed Web of Science ®Google Scholar