401
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Wolf R, Heisenberg M, Brembs B, Waddell S, Mishra A, Kehrer A, Simenson A. Memory, anticipation, action – working with Troy D. Zars. J Neurogenet 2020; 34:9-20. [DOI: 10.1080/01677063.2020.1715976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Reinhard Wolf
- Rudolf-Virchow-Zentrum, University of Würzburg, Würzburg, Germany
| | | | - Björn Brembs
- Institut für Zoologie-Neurogenetik, University of Regensburg, Regensburg, Germany
| | - Scott Waddell
- Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, UK
| | - Aditi Mishra
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Abigail Kehrer
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Angelynn Simenson
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
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402
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403
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Abstract
The field has successfully used Drosophila genetic tools to identify neurons and sub-circuits important for specific functions. However, for an organism with complex and changing internal states to succeed in a complex and changing natural environment, many neurons and circuits need to interact dynamically. Drosophila's many advantages, combined with new imaging tools, offer unique opportunities to study how the brain functions as a complex dynamical system. We give an overview of complex activity patterns and how they can be observed, as well as modeling strategies, adding proof of principle in some cases.
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Affiliation(s)
- Sophie Aimon
- School of Life Sciences, Technical University of Munich, Freising, Germany
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404
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Collins LT. The case for emulating insect brains using anatomical "wiring diagrams" equipped with biophysical models of neuronal activity. BIOLOGICAL CYBERNETICS 2019; 113:465-474. [PMID: 31696303 DOI: 10.1007/s00422-019-00810-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
Developing whole-brain emulation (WBE) technology would provide immense benefits across neuroscience, biomedicine, artificial intelligence, and robotics. At this time, constructing a simulated human brain lacks feasibility due to limited experimental data and limited computational resources. However, I suggest that progress toward this goal might be accelerated by working toward an intermediate objective, namely insect brain emulation (IBE). More specifically, this would entail creating biologically realistic simulations of entire insect nervous systems along with more approximate simulations of non-neuronal insect physiology to make "virtual insects." I argue that this could be realistically achievable within the next 20 years. I propose that developing emulations of insect brains will galvanize the global community of scientists, businesspeople, and policymakers toward pursuing the loftier goal of emulating the human brain. By demonstrating that WBE is possible via IBE, simulating mammalian brains and eventually the human brain may no longer be viewed as too radically ambitious to deserve substantial funding and resources. Furthermore, IBE will facilitate dramatic advances in cognitive neuroscience, artificial intelligence, and robotics through studies performed using virtual insects.
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Affiliation(s)
- Logan T Collins
- Department of Psychology and Neuroscience, University of Colorado, Boulder, 2860 Wilderness Place, Boulder, CO, 80301, USA.
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405
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Sherer LM, Certel SJ. The fight to understand fighting: neurogenetic approaches to the study of aggression in insects. CURRENT OPINION IN INSECT SCIENCE 2019; 36:18-24. [PMID: 31302354 PMCID: PMC6906251 DOI: 10.1016/j.cois.2019.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/14/2019] [Accepted: 06/12/2019] [Indexed: 06/10/2023]
Abstract
Aggression is an evolutionarily conserved behavior that evolved in the framework of defending or obtaining resources. When expressed out of context, unchecked aggression can have destructive consequences. Model systems that allow examination of distinct neuronal networks at the molecular, cellular, and circuit levels are adding immensely to our understanding of the biological basis of this behavior and should be relatable to other species up to and including man. Investigators have made particular use of insect models to both describe this quantifiable and stereotyped behavior and to manipulate genes and neuron function via numerous genetic and pharmacological tools. This review discusses recent advances in techniques that improve our ability to identify, manipulate, visualize, and compare the genes, neurons, and circuits that are required for the output of this complex and clinically relevant social behavior.
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Affiliation(s)
- Lewis M Sherer
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, United States
| | - Sarah J Certel
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, United States.
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406
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Amin H, Lin AC. Neuronal mechanisms underlying innate and learned olfactory processing in Drosophila. CURRENT OPINION IN INSECT SCIENCE 2019; 36:9-17. [PMID: 31280185 DOI: 10.1016/j.cois.2019.06.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
Olfaction allows animals to adapt their behavior in response to different chemical cues in their environment. How does the brain efficiently discriminate different odors to drive appropriate behavior, and how does it flexibly assign value to odors to adjust behavior according to experience? This review traces neuronal mechanisms underlying these processes in adult Drosophila melanogaster from olfactory receptors to higher brain centers. We highlight neural circuit principles such as lateral inhibition, segregation and integration of olfactory channels, temporal accumulation of sensory evidence, and compartmentalized synaptic plasticity underlying associative memory.
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Affiliation(s)
- Hoger Amin
- Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Andrew C Lin
- Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom.
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407
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Mahishi D, Huetteroth W. The prandial process in flies. CURRENT OPINION IN INSECT SCIENCE 2019; 36:157-166. [PMID: 31765996 DOI: 10.1016/j.cois.2019.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/03/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Feeding is fundamental to any heterotroph organism; in its role to quell hunger it overrides most other motivational states. But feeding also literally opens the door to harmful risks, especially for a saprophagous animal like Drosophila; ingestion of poisonous substrate can lead to irreversible damage. Thus feeding incorporates a series of steps with several checkpoints to guarantee that the ingestion remains beneficial and provides a balanced diet, or the feeding process is interrupted. Subsequently, we will summarize and describe the feeding process in Drosophila in a comprehensive manner. We propose eleven distinct steps for feeding, grouped into four categories, to address our current knowledge of prandial regulatory mechanisms in Drosophila.
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Affiliation(s)
- Deepthi Mahishi
- Department of Biology, University of Leipzig, Leipzig, Germany
| | - Wolf Huetteroth
- Department of Biology, University of Leipzig, Leipzig, Germany.
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408
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Selcho M, Pauls D. Linking physiological processes and feeding behaviors by octopamine. CURRENT OPINION IN INSECT SCIENCE 2019; 36:125-130. [PMID: 31606580 DOI: 10.1016/j.cois.2019.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/09/2019] [Indexed: 05/21/2023]
Abstract
The biogenic amine octopamine and to some extent its precursor tyramine function as an alerting signal in insects. Octopaminergic/tyraminergic neurons arborize in most parts of the central nervous system and additionally reach almost all peripheral organs, tissues, and muscles. Indeed, octopamine is involved in motivation, arousal, and the initiation of different behaviors reflecting its function as an alerting signal. A well-studied example of octopamine function is feeding behavior in Drosophila. Here, the amine is involved in food search, sugar/bitter sensitivity, food intake, and starvation-induced hyperactivity. Thereby octopamine modulates feeding initiation in response to internal needs and external stimuli. Additionally, it seems that octopamine/tyramine orchestrate behaviors such as locomotion and feeding or flight and song production to adapt the behavioral outcome of an animal to physiological and environmental conditions. There is a possibility that octopamine and tyramine are required in the selection of behaviors in insects.
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Affiliation(s)
- Mareike Selcho
- Neurobiology and Genetics, Theodor-Boveri-Institute Biocenter, University of Würzburg, Würzburg, Germany; Department of Animal Physiology, Institute of Biology, Leipzig University, Leipzig, Germany.
| | - Dennis Pauls
- Neurobiology and Genetics, Theodor-Boveri-Institute Biocenter, University of Würzburg, Würzburg, Germany; Department of Animal Physiology, Institute of Biology, Leipzig University, Leipzig, Germany.
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409
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Ahrens MB. Zebrafish Neuroscience: Using Artificial Neural Networks to Help Understand Brains. Curr Biol 2019; 29:R1138-R1140. [PMID: 31689401 DOI: 10.1016/j.cub.2019.09.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Brains are notoriously hard to understand, and neuroscientists need all the tools they can get their hands on to have a realistic shot at it. Advances in machine learning are proving instrumental, illustrated by their recent use to shed light on navigational strategies implemented by zebrafish brains.
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Affiliation(s)
- Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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410
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411
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Pape C, Matskevych A, Wolny A, Hennies J, Mizzon G, Louveaux M, Musser J, Maizel A, Arendt D, Kreshuk A. Leveraging Domain Knowledge to Improve Microscopy Image Segmentation With Lifted Multicuts. FRONTIERS IN COMPUTER SCIENCE 2019. [DOI: 10.3389/fcomp.2019.00006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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412
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Städele C, Rimniceanu M, Frye MA. Drosophila Neuroscience: Should I Land or Should I Jump? Curr Biol 2019; 29:R1089-R1091. [PMID: 31639356 DOI: 10.1016/j.cub.2019.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Information about behavioral states can be integrated in decision-making circuits. In Drosophila, the behavioral state - flying versus not flying - determines whether flies land or jump by dynamically coupling visual information to pre-motor descending neurons.
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Affiliation(s)
- Carola Städele
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095, USA.
| | - Martha Rimniceanu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095, USA
| | - Mark A Frye
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095, USA
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413
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Shinomiya K, Horne JA, McLin S, Wiederman M, Nern A, Plaza SM, Meinertzhagen IA. The Organization of the Second Optic Chiasm of the Drosophila Optic Lobe. Front Neural Circuits 2019; 13:65. [PMID: 31680879 PMCID: PMC6797552 DOI: 10.3389/fncir.2019.00065] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 09/27/2019] [Indexed: 01/03/2023] Open
Abstract
Visual pathways from the compound eye of an insect relay to four neuropils, successively the lamina, medulla, lobula, and lobula plate in the underlying optic lobe. Among these neuropils, the medulla, lobula, and lobula plate are interconnected by the complex second optic chiasm, through which the anteroposterior axis undergoes an inversion between the medulla and lobula. Given their complex structure, the projection patterns through the second optic chiasm have so far lacked critical analysis. By densely reconstructing axon trajectories using a volumetric scanning electron microscopy (SEM) technique, we reveal the three-dimensional structure of the second optic chiasm of Drosophila melanogaster, which comprises interleaving bundles and sheets of axons insulated from each other by glial sheaths. These axon bundles invert their horizontal sequence in passing between the medulla and lobula. Axons connecting the medulla and lobula plate are also bundled together with them but do not decussate the sequence of their horizontal positions. They interleave with sheets of projection neuron axons between the lobula and lobula plate, which also lack decussations. We estimate that approximately 19,500 cells per hemisphere, about two thirds of the optic lobe neurons, contribute to the second chiasm, most being Tm cells, with an estimated additional 2,780 T4 and T5 cells each. The chiasm mostly comprises axons and cell body fibers, but also a few synaptic elements. Based on our anatomical findings, we propose that a chiasmal structure between the neuropils is potentially advantageous for processing complex visual information in parallel. The EM reconstruction shows not only the structure of the chiasm in the adult brain, the previously unreported main topic of our study, but also suggest that the projection patterns of the neurons comprising the chiasm may be determined by the proliferation centers from which the neurons develop. Such a complex wiring pattern could, we suggest, only have arisen in several evolutionary steps.
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Affiliation(s)
| | - Jane Anne Horne
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, Canada
| | - Sari McLin
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, Canada
| | - Meagan Wiederman
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, Canada
| | - Aljoscha Nern
- Howard Hughes Medical Institute, Ashburn, VA, United States
| | | | - Ian A Meinertzhagen
- Howard Hughes Medical Institute, Ashburn, VA, United States.,Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, Canada
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414
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Loomis C, Peuß R, Jaggard JB, Wang Y, McKinney SA, Raftopoulos SC, Raftopoulos A, Whu D, Green M, McGaugh SE, Rohner N, Keene AC, Duboue ER. An Adult Brain Atlas Reveals Broad Neuroanatomical Changes in Independently Evolved Populations of Mexican Cavefish. Front Neuroanat 2019; 13:88. [PMID: 31636546 PMCID: PMC6788135 DOI: 10.3389/fnana.2019.00088] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/11/2019] [Indexed: 01/08/2023] Open
Abstract
A shift in environmental conditions impacts the evolution of complex developmental and behavioral traits. The Mexican cavefish, Astyanax mexicanus, is a powerful model for examining the evolution of development, physiology, and behavior because multiple cavefish populations can be compared to an extant, ancestral-like surface population of the same species. Many behaviors have diverged in cave populations of A. mexicanus, and previous studies have shown that cavefish have a loss of sleep, reduced stress, an absence of social behaviors, and hyperphagia. Despite these findings, surprisingly little is known about the changes in neuroanatomy that underlie these behavioral phenotypes. Here, we use serial sectioning to generate brain atlases of surface fish and three independent cavefish populations. Volumetric reconstruction of serial-sectioned brains confirms convergent evolution on reduced optic tectum volume in all cavefish populations tested. In addition, we quantified volumes of specific neuroanatomical loci within several brain regions that have previously been implicated in behavioral regulation, including the hypothalamus, thalamus, and habenula. These analyses reveal an enlargement of the hypothalamus in all cavefish populations relative to surface fish, as well as subnuclei-specific differences within the thalamus and prethalamus. Taken together, these analyses support the notion that changes in environmental conditions are accompanied by neuroanatomical changes in brain structures associated with behavior. This atlas provides a resource for comparative neuroanatomy of additional brain regions and the opportunity to associate brain anatomy with evolved changes in behavior.
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Affiliation(s)
- Cody Loomis
- Department of Biology, Charles E. Schmidt College of Science, Florida Atlantic University, Jupiter, FL, United States
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL, United States
| | - Robert Peuß
- Stowers Institute for Medical Research, Kansas City, MO, United States
| | - James B. Jaggard
- Department of Biology, Charles E. Schmidt College of Science, Florida Atlantic University, Jupiter, FL, United States
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL, United States
| | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas City, MO, United States
| | - Sean A. McKinney
- Stowers Institute for Medical Research, Kansas City, MO, United States
| | - Stephan C. Raftopoulos
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL, United States
| | - Austin Raftopoulos
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL, United States
| | - Daniel Whu
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL, United States
| | - Matthew Green
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL, United States
| | - Suzanne E. McGaugh
- Department of Ecology, University of Minnesota, St. Paul, MN, United States
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Molecular and Integrative Physiology, KU Medical Center, Kansas City, KS, United States
| | - Alex C. Keene
- Department of Biology, Charles E. Schmidt College of Science, Florida Atlantic University, Jupiter, FL, United States
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL, United States
| | - Erik R. Duboue
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL, United States
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL, United States
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415
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Rings A, Goodwin SF. To court or not to court - a multimodal sensory decision in Drosophila males. CURRENT OPINION IN INSECT SCIENCE 2019; 35:48-53. [PMID: 31336357 DOI: 10.1016/j.cois.2019.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 06/10/2023]
Abstract
When Drosophila males encounter another fly, they have to make a rapid assessment to ensure the appropriate response: should they court, fight or pursue a different action entirely? Previous work has focused on the significance of sensory cues detected by the male during these encounters; however, recent evidence highlights the importance of the male's own internal state in shaping his responses. Additionally, once triggered, courtship is not a rigid sequence of motor actions, but rather a finely tuned behavioural display that must continually update in response to sensory feedback. Here, we review recent findings highlighting how sensory information and internal states are integrated ensuring appropriate action selection, and how they sustain and fine-tune motor output. We further discuss recent advances in our understanding of species differences in sensory processing that may contribute to reproductive isolation.
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Affiliation(s)
- Annika Rings
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford, OX1 3SR, UK.
| | - Stephen F Goodwin
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford, OX1 3SR, UK
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416
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3D cellular reconstruction of cortical glia and parenchymal morphometric analysis from Serial Block-Face Electron Microscopy of juvenile rat. Prog Neurobiol 2019; 183:101696. [PMID: 31550514 DOI: 10.1016/j.pneurobio.2019.101696] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 01/04/2023]
Abstract
With the rapid evolution in the automation of serial electron microscopy in life sciences, the acquisition of terabyte-sized datasets is becoming increasingly common. High resolution serial block-face imaging (SBEM) of biological tissues offers the opportunity to segment and reconstruct nanoscale structures to reveal spatial features previously inaccessible with simple, single section, two-dimensional images. In particular, we focussed here on glial cells, whose reconstruction efforts in literature are still limited, compared to neurons. We imaged a 750,000 cubic micron volume of the somatosensory cortex from a juvenile P14 rat, with 20 nm accuracy. We recognized a total of 186 cells using their nuclei, and classified them as neuronal or glial based on features of the soma and the processes. We reconstructed for the first time 4 almost complete astrocytes and neurons, 4 complete microglia and 4 complete pericytes, including their intracellular mitochondria, 186 nuclei and 213 myelinated axons. We then performed quantitative analysis on the three-dimensional models. Out of the data that we generated, we observed that neurons have larger nuclei, which correlated with their lesser density, and that astrocytes and pericytes have a higher surface to volume ratio, compared to other cell types. All reconstructed morphologies represent an important resource for computational neuroscientists, as morphological quantitative information can be inferred, to tune simulations that take into account the spatial compartmentalization of the different cell types.
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417
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Molina-Obando S, Vargas-Fique JF, Henning M, Gür B, Schladt TM, Akhtar J, Berger TK, Silies M. ON selectivity in the Drosophila visual system is a multisynaptic process involving both glutamatergic and GABAergic inhibition. eLife 2019; 8:e49373. [PMID: 31535971 PMCID: PMC6845231 DOI: 10.7554/elife.49373] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 09/18/2019] [Indexed: 01/06/2023] Open
Abstract
Sensory systems sequentially extract increasingly complex features. ON and OFF pathways, for example, encode increases or decreases of a stimulus from a common input. This ON/OFF pathway split is thought to occur at individual synaptic connections through a sign-inverting synapse in one of the pathways. Here, we show that ON selectivity is a multisynaptic process in the Drosophila visual system. A pharmacogenetics approach demonstrates that both glutamatergic inhibition through GluClα and GABAergic inhibition through Rdl mediate ON responses. Although neurons postsynaptic to the glutamatergic ON pathway input L1 lose all responses in GluClα mutants, they are resistant to a cell-type-specific loss of GluClα. This shows that ON selectivity is distributed across multiple synapses, and raises the possibility that cell-type-specific manipulations might reveal similar strategies in other sensory systems. Thus, sensory coding is more distributed than predicted by simple circuit motifs, allowing for robust neural processing.
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Affiliation(s)
- Sebastian Molina-Obando
- Institute of Developmental Biology and NeurobiologyJohannes Gutenberg-Universität MainzMainzGermany
- European Neuroscience Institute Göttingen – A Joint Initiative of the University Medical Center Göttingen and the Max-Planck-SocietyGöttingenGermany
- International Max Planck Research School and Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB) at the University of GöttingenGöttingenGermany
| | - Juan Felipe Vargas-Fique
- Institute of Developmental Biology and NeurobiologyJohannes Gutenberg-Universität MainzMainzGermany
- European Neuroscience Institute Göttingen – A Joint Initiative of the University Medical Center Göttingen and the Max-Planck-SocietyGöttingenGermany
- International Max Planck Research School and Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB) at the University of GöttingenGöttingenGermany
| | - Miriam Henning
- Institute of Developmental Biology and NeurobiologyJohannes Gutenberg-Universität MainzMainzGermany
- European Neuroscience Institute Göttingen – A Joint Initiative of the University Medical Center Göttingen and the Max-Planck-SocietyGöttingenGermany
| | - Burak Gür
- Institute of Developmental Biology and NeurobiologyJohannes Gutenberg-Universität MainzMainzGermany
- European Neuroscience Institute Göttingen – A Joint Initiative of the University Medical Center Göttingen and the Max-Planck-SocietyGöttingenGermany
- International Max Planck Research School and Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB) at the University of GöttingenGöttingenGermany
| | - T Moritz Schladt
- Department of Molecular Sensory SystemsCenter of Advanced European Studies and Research (caesar)BonnGermany
| | - Junaid Akhtar
- Institute of Developmental Biology and NeurobiologyJohannes Gutenberg-Universität MainzMainzGermany
| | - Thomas K Berger
- Department of Molecular Sensory SystemsCenter of Advanced European Studies and Research (caesar)BonnGermany
- Institute of Physiology and PathophysiologyPhilipps-Universität MarburgMarburgGermany
| | - Marion Silies
- Institute of Developmental Biology and NeurobiologyJohannes Gutenberg-Universität MainzMainzGermany
- European Neuroscience Institute Göttingen – A Joint Initiative of the University Medical Center Göttingen and the Max-Planck-SocietyGöttingenGermany
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418
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Constraining computational models using electron microscopy wiring diagrams. Curr Opin Neurobiol 2019; 58:94-100. [PMID: 31470252 DOI: 10.1016/j.conb.2019.07.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/25/2019] [Indexed: 12/18/2022]
Abstract
Numerous efforts to generate "connectomes," or synaptic wiring diagrams, of large neural circuits or entire nervous systems are currently underway. These efforts promise an abundance of data to guide theoretical models of neural computation and test their predictions. However, there is not yet a standard set of tools for incorporating the connectivity constraints that these datasets provide into the models typically studied in theoretical neuroscience. This article surveys recent approaches to building models with constrained wiring diagrams and the insights they have provided. It also describes challenges and the need for new techniques to scale these approaches to ever more complex datasets.
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419
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Siegenthaler D, Escribano B, Bräuler V, Pielage J. Selective suppression and recall of long-term memories in Drosophila. PLoS Biol 2019; 17:e3000400. [PMID: 31454345 PMCID: PMC6711512 DOI: 10.1371/journal.pbio.3000400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 07/22/2019] [Indexed: 11/18/2022] Open
Abstract
Adaptive decision-making depends on the formation of novel memories. In Drosophila, the mushroom body (MB) is the site of associative olfactory long-term memory (LTM) storage. However, due to the sparse and stochastic representation of olfactory information in Kenyon cells (KCs), genetic access to individual LTMs remains elusive. Here, we develop a cAMP response element (CRE)-activity–dependent memory engram label (CAMEL) tool that genetically tags KCs responding to the conditioned stimulus (CS). CAMEL activity depends on protein-synthesis–dependent aversive LTM conditioning and reflects the time course of CRE binding protein 2 (CREB2) activity during natural memory formation. We demonstrate that inhibition of LTM-induced CAMEL neurons reduces memory expression and that artificial optogenetic reactivation is sufficient to evoke aversive behavior phenocopying memory recall. Together, our data are consistent with CAMEL neurons marking a subset of engram KCs encoding individual memories. This study provides new insights into memory circuitry organization and an entry point towards cellular and molecular understanding of LTM storage. A novel genetic approach enables the visualization and manipulation of memory engram cells in Drosophila, providing a key methodological opportunity to characterize associative memory at the cellular and circuit level.
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Affiliation(s)
- Dominique Siegenthaler
- Division of Neurobiology and Zoology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Benjamin Escribano
- Division of Neurobiology and Zoology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Vanessa Bräuler
- Division of Neurobiology and Zoology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jan Pielage
- Division of Neurobiology and Zoology, University of Kaiserslautern, Kaiserslautern, Germany
- * E-mail:
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420
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Sayin S, De Backer JF, Siju KP, Wosniack ME, Lewis LP, Frisch LM, Gansen B, Schlegel P, Edmondson-Stait A, Sharifi N, Fisher CB, Calle-Schuler SA, Lauritzen JS, Bock DD, Costa M, Jefferis GSXE, Gjorgjieva J, Grunwald Kadow IC. A Neural Circuit Arbitrates between Persistence and Withdrawal in Hungry Drosophila. Neuron 2019; 104:544-558.e6. [PMID: 31471123 PMCID: PMC6839618 DOI: 10.1016/j.neuron.2019.07.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/09/2019] [Accepted: 07/22/2019] [Indexed: 01/24/2023]
Abstract
In pursuit of food, hungry animals mobilize significant energy resources and overcome exhaustion and fear. How need and motivation control the decision to continue or change behavior is not understood. Using a single fly treadmill, we show that hungry flies persistently track a food odor and increase their effort over repeated trials in the absence of reward suggesting that need dominates negative experience. We further show that odor tracking is regulated by two mushroom body output neurons (MBONs) connecting the MB to the lateral horn. These MBONs, together with dopaminergic neurons and Dop1R2 signaling, control behavioral persistence. Conversely, an octopaminergic neuron, VPM4, which directly innervates one of the MBONs, acts as a brake on odor tracking by connecting feeding and olfaction. Together, our data suggest a function for the MB in internal state-dependent expression of behavior that can be suppressed by external inputs conveying a competing behavioral drive. Hunger motivates persistent food odor tracking even without reward Two synaptically connected MBONs, -γ1pedc>αβ and -α2sc, regulate odor tracking Octopamine neurons connect feeding and counteract MBON and odor tracking Dopaminergic neurons and Dop1R2 signaling promote persistent tracking
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Affiliation(s)
- Sercan Sayin
- Technical University of Munich, School of Life Sciences, 85354 Freising, Germany
| | | | - K P Siju
- Technical University of Munich, School of Life Sciences, 85354 Freising, Germany
| | - Marina E Wosniack
- Technical University of Munich, School of Life Sciences, 85354 Freising, Germany; Max Planck Institute for Brain Research, Computation in Neural Circuits Group, 60438 Frankfurt, Germany
| | - Laurence P Lewis
- Max Planck Institute of Neurobiology, Chemosensory Coding Group, 82152 Martinsried, Germany
| | - Lisa-Marie Frisch
- Technical University of Munich, School of Life Sciences, 85354 Freising, Germany
| | - Benedikt Gansen
- Technical University of Munich, School of Life Sciences, 85354 Freising, Germany
| | - Philipp Schlegel
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Amelia Edmondson-Stait
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | | | | | | | | | - Davi D Bock
- HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Marta Costa
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Gregory S X E Jefferis
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK; Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Julijana Gjorgjieva
- Technical University of Munich, School of Life Sciences, 85354 Freising, Germany; Max Planck Institute for Brain Research, Computation in Neural Circuits Group, 60438 Frankfurt, Germany
| | - Ilona C Grunwald Kadow
- Technical University of Munich, School of Life Sciences, 85354 Freising, Germany; ZIEL - Institute for food and health, 85354 Freising, Germany; Max Planck Institute of Neurobiology, Chemosensory Coding Group, 82152 Martinsried, Germany.
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421
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Saleeba C, Dempsey B, Le S, Goodchild A, McMullan S. A Student's Guide to Neural Circuit Tracing. Front Neurosci 2019; 13:897. [PMID: 31507369 PMCID: PMC6718611 DOI: 10.3389/fnins.2019.00897] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/12/2019] [Indexed: 12/17/2022] Open
Abstract
The mammalian nervous system is comprised of a seemingly infinitely complex network of specialized synaptic connections that coordinate the flow of information through it. The field of connectomics seeks to map the structure that underlies brain function at resolutions that range from the ultrastructural, which examines the organization of individual synapses that impinge upon a neuron, to the macroscopic, which examines gross connectivity between large brain regions. At the mesoscopic level, distant and local connections between neuronal populations are identified, providing insights into circuit-level architecture. Although neural tract tracing techniques have been available to experimental neuroscientists for many decades, considerable methodological advances have been made in the last 20 years due to synergies between the fields of molecular biology, virology, microscopy, computer science and genetics. As a consequence, investigators now enjoy an unprecedented toolbox of reagents that can be directed against selected subpopulations of neurons to identify their efferent and afferent connectomes. Unfortunately, the intersectional nature of this progress presents newcomers to the field with a daunting array of technologies that have emerged from disciplines they may not be familiar with. This review outlines the current state of mesoscale connectomic approaches, from data collection to analysis, written for the novice to this field. A brief history of neuroanatomy is followed by an assessment of the techniques used by contemporary neuroscientists to resolve mesoscale organization, such as conventional and viral tracers, and methods of selecting for sub-populations of neurons. We consider some weaknesses and bottlenecks of the most widely used approaches for the analysis and dissemination of tracing data and explore the trajectories that rapidly developing neuroanatomy technologies are likely to take.
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Affiliation(s)
- Christine Saleeba
- Neurobiology of Vital Systems Node, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
- The School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Bowen Dempsey
- CNRS, Hindbrain Integrative Neurobiology Laboratory, Neuroscience Paris-Saclay Institute (Neuro-PSI), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Sheng Le
- Neurobiology of Vital Systems Node, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ann Goodchild
- Neurobiology of Vital Systems Node, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Simon McMullan
- Neurobiology of Vital Systems Node, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
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422
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Hall MJR, Martín-Vega D. Visualization of insect metamorphosis. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190071. [PMID: 31438819 DOI: 10.1098/rstb.2019.0071] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Metamorphosis and, in particular, holometaboly, the development of organisms through a series of discrete stages (egg, larva, pupa, adult) that hardly resemble one another but are finely adapted to specific roles in the life cycle of the organism, has fascinated and mystified humans throughout history. However, it can be difficult to visualize the dramatic changes that occur during holometaboly without destructive sampling, traditionally through histology. However, advances in imaging technologies developed mainly for medical sciences have been applied to studies of insect metamorphosis over the past couple of decades. These include micro-computed tomography, magnetic resonance imaging and optical coherence tomography. A major advantage of these techniques is that they are rapid and non-destructive, enabling virtual dissection of an organism in any plane by anyone who has access to the image files and the necessary software. They can also be applied in some cases to visualize metamorphosis in vivo, including the periods of most rapid and dramatic morphological change. This review focusses on visualizing the intra-puparial holometabolous metamorphosis of cyclorraphous flies (Diptera), including the primary model organism for all genetic investigations, Drosophila melanogaster, and the blow flies of medical, veterinary and forensic importance, but also discusses similar studies on other insect orders. This article is part of the theme issue 'The evolution of complete metamorphosis'.
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Affiliation(s)
- Martin J R Hall
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Daniel Martín-Vega
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.,Department of Life Sciences, University of Alcalá, Alcalá de Henares, Spain
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423
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Bloss EB, Hunt DL. Revealing the Synaptic Hodology of Mammalian Neural Circuits With Multiscale Neurocartography. Front Neuroinform 2019; 13:52. [PMID: 31427940 PMCID: PMC6690003 DOI: 10.3389/fninf.2019.00052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
The functional features of neural circuits are determined by a combination of properties that range in scale from projections systems across the whole brain to molecular interactions at the synapse. The burgeoning field of neurocartography seeks to map these relevant features of brain structure—spanning a volume ∼20 orders of magnitude—to determine how neural circuits perform computations supporting cognitive function and complex behavior. Recent technological breakthroughs in tissue sample preparation, high-throughput electron microscopy imaging, and automated image analyses have produced the first visualizations of all synaptic connections between neurons of invertebrate model systems. However, the sheer size of the central nervous system in mammals implies that reconstruction of the first full brain maps at synaptic scale may not be feasible for decades. In this review, we outline existing and emerging technologies for neurocartography that complement electron microscopy-based strategies and are beginning to derive some basic organizing principles of circuit hodology at the mesoscale, microscale, and nanoscale. Specifically, we discuss how a host of light microscopy techniques including array tomography have been utilized to determine both long-range and subcellular organizing principles of synaptic connectivity. In addition, we discuss how new techniques, such as two-photon serial tomography of the entire mouse brain, have become attractive approaches to dissect the potential connectivity of defined cell types. Ultimately, principles derived from these techniques promise to facilitate a conceptual understanding of how connectomes, and neurocartography in general, can be effectively utilized toward reaching a mechanistic understanding of circuit function.
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Affiliation(s)
- Erik B Bloss
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, United States
| | - David L Hunt
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, United States
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424
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Boto T, Tomchik SM. The Excitatory, the Inhibitory, and the Modulatory: Mapping Chemical Neurotransmission in the Brain. Neuron 2019; 101:763-765. [PMID: 30844392 DOI: 10.1016/j.neuron.2019.02.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this issue of Neuron, Deng et al. (2019) report the generation of a new set of tools to manipulate the entire set of neurotransmitters, neuromodulators, neuropeptides, and their receptors-the "chemoconnectome"-in Drosophila.
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Affiliation(s)
- Tamara Boto
- The Scripps Research Institute, Scripps Florida, Department of Neuroscience, 130 Scripps Way #3C1, Jupiter, FL 33458, USA
| | - Seth M Tomchik
- The Scripps Research Institute, Scripps Florida, Department of Neuroscience, 130 Scripps Way #3C1, Jupiter, FL 33458, USA.
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425
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Boulgakov AA, Ellington AD, Marcotte EM. Bringing Microscopy-By-Sequencing into View. Trends Biotechnol 2019; 38:154-162. [PMID: 31416630 DOI: 10.1016/j.tibtech.2019.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 01/07/2023]
Abstract
The spatial distribution of molecules and cells is fundamental to understanding biological systems. Traditionally, microscopies based on electromagnetic waves such as visible light have been used to localize cellular components by direct visualization. However, these techniques suffer from limitations of transmissibility and throughput. Complementary to optical approaches, biochemical techniques such as crosslinking can colocalize molecules without suffering the same limitations. However, biochemical approaches are often unable to combine individual colocalizations into a map across entire cells or tissues. Microscopy-by-sequencing techniques aim to biochemically colocalize DNA-barcoded molecules and, by tracking their thus unique identities, reconcile all colocalizations into a global spatial map. Here, we review this new field and discuss its enormous potential to answer a broad spectrum of questions.
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Affiliation(s)
- Alexander A Boulgakov
- Center for Systems and Synthetic Biology, Institute of Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Institute of Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Edward M Marcotte
- Center for Systems and Synthetic Biology, Institute of Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
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426
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Sigmund F, Pettinger S, Kube M, Schneider F, Schifferer M, Schneider S, Efremova MV, Pujol-Martí J, Aichler M, Walch A, Misgeld T, Dietz H, Westmeyer GG. Iron-Sequestering Nanocompartments as Multiplexed Electron Microscopy Gene Reporters. ACS NANO 2019; 13:8114-8123. [PMID: 31194509 DOI: 10.1021/acsnano.9b03140] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Multicolored gene reporters for light microscopy are indispensable for biomedical research, but equivalent genetic tools for electron microscopy (EM) are still rare despite the increasing importance of nanometer resolution for reverse engineering of molecular machinery and reliable mapping of cellular circuits. We here introduce the fully genetic encapsulin/cargo system of Quasibacillus thermotolerans (Qt), which in combination with the recently characterized encapsulin system from Myxococcus xanthus (Mx) enables multiplexed gene reporter imaging via conventional transmission electron microscopy (TEM) in mammalian cells. Cryo-electron reconstructions revealed that the Qt encapsulin shell self-assembles to nanospheres with T = 4 icosahedral symmetry and a diameter of ∼43 nm harboring two putative pore regions at the 5-fold and 3-fold axes. We also found that upon heterologous expression in mammalian cells, the native cargo is autotargeted to the inner surface of the shell and exhibits ferroxidase activity leading to efficient intraluminal iron biomineralization, which enhances cellular TEM contrast. We furthermore demonstrate that the two differently sized encapsulins of Qt and Mx do not intermix and can be robustly differentiated by conventional TEM via a deep learning classifier to enable automated multiplexed EM gene reporter imaging.
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Affiliation(s)
- Felix Sigmund
- Department of Nuclear Medicine, TUM School of Medicine , Technical University of Munich , 81675 Munich , Germany
- Institute of Biological and Medical Imaging , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Institute of Developmental Genetics , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Susanne Pettinger
- Department of Nuclear Medicine, TUM School of Medicine , Technical University of Munich , 81675 Munich , Germany
- Institute of Biological and Medical Imaging , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Institute of Developmental Genetics , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Massimo Kube
- Laboratory for Biomolecular Design, Department of Physics , Technical University of Munich , 85748 Garching , Germany
| | - Fabian Schneider
- Laboratory for Biomolecular Design, Department of Physics , Technical University of Munich , 85748 Garching , Germany
| | - Martina Schifferer
- Institute of Neuronal Cell Biology, TUM School of Medicine , Technical University of Munich , 80802 Munich , Germany
- German Center for Neurodegenerative Diseases (DZNE) , 81377 Munich , Germany
| | - Steffen Schneider
- Computational Neuroengineering, Department of Electrical and Computer Engineering , Technical University of Munich , 80333 Munich , Germany
- Tübingen AI Center , University of Tübingen , 72076 Tübingen , Germany
| | - Maria V Efremova
- Department of Nuclear Medicine, TUM School of Medicine , Technical University of Munich , 81675 Munich , Germany
- Institute of Biological and Medical Imaging , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Institute of Developmental Genetics , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Laboratory of Chemical Design of Bionanomaterials for Medical Applications, Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russian Federation
| | - Jesús Pujol-Martí
- Department "Circuits - Computation - Models" , Max Planck Institute of Neurobiology , 82152 Martinsried , Germany
| | - Michaela Aichler
- Research Unit Analytical Pathology , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Axel Walch
- Research Unit Analytical Pathology , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Thomas Misgeld
- Institute of Neuronal Cell Biology, TUM School of Medicine , Technical University of Munich , 80802 Munich , Germany
- German Center for Neurodegenerative Diseases (DZNE) , 81377 Munich , Germany
| | - Hendrik Dietz
- Laboratory for Biomolecular Design, Department of Physics , Technical University of Munich , 85748 Garching , Germany
| | - Gil G Westmeyer
- Department of Nuclear Medicine, TUM School of Medicine , Technical University of Munich , 81675 Munich , Germany
- Institute of Biological and Medical Imaging , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Institute of Developmental Genetics , Helmholtz Zentrum München , 85764 Neuherberg , Germany
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427
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Templier T. MagC, magnetic collection of ultrathin sections for volumetric correlative light and electron microscopy. eLife 2019; 8:e45696. [PMID: 31294691 PMCID: PMC6697447 DOI: 10.7554/elife.45696] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/02/2019] [Indexed: 01/03/2023] Open
Abstract
The non-destructive collection of ultrathin sections on silicon wafers for post-embedding staining and volumetric correlative light and electron microscopy traditionally requires exquisite manual skills and is tedious and unreliable. In MagC introduced here, sample blocks are augmented with a magnetic resin enabling the remote actuation and collection of hundreds of sections on wafer. MagC allowed the correlative visualization of neuroanatomical tracers within their ultrastructural volumetric electron microscopy context.
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Affiliation(s)
- Thomas Templier
- Institute of NeuroinformaticsUniversity of Zurich and ETH ZurichZurichSwitzerland
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428
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Abstract
The brain's synaptic networks endow an animal with powerfully adaptive biological behavior. Maps of such synaptic circuits densely reconstructed in those model brains that can be examined and manipulated by genetic means offer the best prospect for understanding the underlying biological bases of behavior. That prospect is now technologically feasible and a scientifically enabling possibility in neurobiology, much as genomics has been in molecular biology and genetics. In Drosophila, two major advances are in electron microscopic technology, using focused ion beam-scanning electron microscopy (FIB-SEM) milling to capture and align digital images, and in computer-aided reconstruction of neuron morphologies. The last decade has witnessed enormous progress in detailed knowledge of the actual synaptic circuits formed by real neurons. Advances in various brain regions that heralded identification of the motion-sensing circuits in the optic lobe are now extending to other brain regions, with the prospect of encompassing the fly's entire nervous system, both brain and ventral nerve cord.
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Affiliation(s)
- Louis K Scheffer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147-2408, USA;
| | - Ian A Meinertzhagen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147-2408, USA; .,Department of Psychology and Neuroscience and Department of Biology, Life Sciences Centre, Dalhousie University, Halifax, Canada B3H 4R2
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429
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Zhang X, Coates K, Dacks A, Günay C, Lauritzen JS, Li F, Calle-Schuler SA, Bock D, Gaudry Q. Local synaptic inputs support opposing, network-specific odor representations in a widely projecting modulatory neuron. eLife 2019; 8:46839. [PMID: 31264962 PMCID: PMC6660217 DOI: 10.7554/elife.46839] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/01/2019] [Indexed: 12/14/2022] Open
Abstract
Serotonin plays different roles across networks within the same sensory modality. Previously, we used whole-cell electrophysiology in Drosophila to show that serotonergic neurons innervating the first olfactory relay are inhibited by odorants (Zhang and Gaudry, 2016). Here we show that network-spanning serotonergic neurons segregate information about stimulus features, odor intensity and identity, by using opposing coding schemes in different olfactory neuropil. A pair of serotonergic neurons (the CSDns) innervate the antennal lobe and lateral horn, which are first and second order neuropils. CSDn processes in the antennal lobe are inhibited by odors in an identity independent manner. In the lateral horn, CSDn processes are excited in an odor identity dependent manner. Using functional imaging, modeling, and EM reconstruction, we demonstrate that antennal lobe derived inhibition arises from local GABAergic inputs and acts as a means of gain control on branch-specific inputs that the CSDns receive within the lateral horn.
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Affiliation(s)
- Xiaonan Zhang
- Department of Biology, University of Maryland, College Park, United States
| | - Kaylynn Coates
- Department of Biology, West Virginia University, Morgantown, United States
| | - Andrew Dacks
- Department of Biology, West Virginia University, Morgantown, United States
| | - Cengiz Günay
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, United States
| | - J Scott Lauritzen
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Feng Li
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | | | - Davi Bock
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Department of Neurological Sciences, Larner College of Medicine, University of Vermont, Burlington, United States
| | - Quentin Gaudry
- Department of Biology, University of Maryland, College Park, United States
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430
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Acarón Ledesma H, Li X, Carvalho-de-Souza JL, Wei W, Bezanilla F, Tian B. An atlas of nano-enabled neural interfaces. NATURE NANOTECHNOLOGY 2019; 14:645-657. [PMID: 31270446 PMCID: PMC6800006 DOI: 10.1038/s41565-019-0487-x] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/17/2019] [Indexed: 05/19/2023]
Abstract
Advances in microscopy and molecular strategies have allowed researchers to gain insight into the intricate organization of the mammalian brain and the roles that neurons play in processing information. Despite vast progress, therapeutic strategies for neurological disorders remain limited, owing to a lack of biomaterials for sensing and modulating neuronal signalling in vivo. Therefore, there is a pressing need for developing material-based tools that can form seamless biointerfaces and interrogate the brain with unprecedented resolution. In this Review, we discuss important considerations in material design and implementation, highlight recent breakthroughs in neural sensing and modulation, and propose future directions in neurotechnology research. Our goal is to create an atlas for nano-enabled neural interfaces and to demonstrate how emerging nanotechnologies can interrogate neural systems spanning multiple biological length scales.
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Affiliation(s)
- Héctor Acarón Ledesma
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Xiaojian Li
- Brain Cognition and Brain Disease Institute of Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
- Shenzhen-Hongkong Institute of Brain Science, Shenzhen, People's Republic of China
| | - João L Carvalho-de-Souza
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Department of Anesthesiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Wei Wei
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
| | - Francisco Bezanilla
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Centro Interdisciplinario de Neurociencias, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Bozhi Tian
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
- Department of Chemistry, University of Chicago, Chicago, IL, USA.
- James Franck Institute, University of Chicago, Chicago, IL, USA.
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431
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Recanatesi S, Ocker GK, Buice MA, Shea-Brown E. Dimensionality in recurrent spiking networks: Global trends in activity and local origins in connectivity. PLoS Comput Biol 2019; 15:e1006446. [PMID: 31299044 PMCID: PMC6655892 DOI: 10.1371/journal.pcbi.1006446] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 07/24/2019] [Accepted: 04/03/2019] [Indexed: 11/25/2022] Open
Abstract
The dimensionality of a network's collective activity is of increasing interest in neuroscience. This is because dimensionality provides a compact measure of how coordinated network-wide activity is, in terms of the number of modes (or degrees of freedom) that it can independently explore. A low number of modes suggests a compressed low dimensional neural code and reveals interpretable dynamics [1], while findings of high dimension may suggest flexible computations [2, 3]. Here, we address the fundamental question of how dimensionality is related to connectivity, in both autonomous and stimulus-driven networks. Working with a simple spiking network model, we derive three main findings. First, the dimensionality of global activity patterns can be strongly, and systematically, regulated by local connectivity structures. Second, the dimensionality is a better indicator than average correlations in determining how constrained neural activity is. Third, stimulus evoked neural activity interacts systematically with neural connectivity patterns, leading to network responses of either greater or lesser dimensionality than the stimulus.
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Affiliation(s)
- Stefano Recanatesi
- Center for Computational Neuroscience, University of Washington, Seattle, Washington, United States of America
| | - Gabriel Koch Ocker
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Michael A. Buice
- Center for Computational Neuroscience, University of Washington, Seattle, Washington, United States of America
- Allen Institute for Brain Science, Seattle, Washington, United States of America
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America
| | - Eric Shea-Brown
- Center for Computational Neuroscience, University of Washington, Seattle, Washington, United States of America
- Allen Institute for Brain Science, Seattle, Washington, United States of America
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America
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432
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Kunst M, Laurell E, Mokayes N, Kramer A, Kubo F, Fernandes AM, Förster D, Dal Maschio M, Baier H. A Cellular-Resolution Atlas of the Larval Zebrafish Brain. Neuron 2019; 103:21-38.e5. [DOI: 10.1016/j.neuron.2019.04.034] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 04/10/2019] [Accepted: 04/23/2019] [Indexed: 02/06/2023]
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433
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Bielopolski N, Amin H, Apostolopoulou AA, Rozenfeld E, Lerner H, Huetteroth W, Lin AC, Parnas M. Inhibitory muscarinic acetylcholine receptors enhance aversive olfactory learning in adult Drosophila. eLife 2019; 8:48264. [PMID: 31215865 PMCID: PMC6641838 DOI: 10.7554/elife.48264] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/18/2019] [Indexed: 11/13/2022] Open
Abstract
Olfactory associative learning in Drosophila is mediated by synaptic plasticity between the Kenyon cells of the mushroom body and their output neurons. Both Kenyon cells and their inputs from projection neurons are cholinergic, yet little is known about the physiological function of muscarinic acetylcholine receptors in learning in adult flies. Here, we show that aversive olfactory learning in adult flies requires type A muscarinic acetylcholine receptors (mAChR-A), particularly in the gamma subtype of Kenyon cells. mAChR-A inhibits odor responses and is localized in Kenyon cell dendrites. Moreover, mAChR-A knockdown impairs the learning-associated depression of odor responses in a mushroom body output neuron. Our results suggest that mAChR-A function in Kenyon cell dendrites is required for synaptic plasticity between Kenyon cells and their output neurons.
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Affiliation(s)
- Noa Bielopolski
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hoger Amin
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | | | - Eyal Rozenfeld
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hadas Lerner
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Wolf Huetteroth
- Institute for Biology, University of Leipzig, Leipzig, Germany
| | - Andrew C Lin
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Moshe Parnas
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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434
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Kebschull JM. DNA sequencing in high-throughput neuroanatomy. J Chem Neuroanat 2019; 100:101653. [PMID: 31173871 DOI: 10.1016/j.jchemneu.2019.101653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/30/2019] [Accepted: 05/24/2019] [Indexed: 01/15/2023]
Abstract
Mapping brain connectivity at single cell resolution is critical for understanding brain structure. For decades, such mapping has been principally approached with microscopy techniques, aiming to visualize neurons and their connections. However, these techniques are often very labor intensive and do not scale well to the complexity of mammalian brains. We recently leveraged the speed and parallelization of DNA sequencing to map the projections of thousands of single neurons in single experiments, and to map cortical mesoscale connectivity in single mice. Here, I review the state of sequencing-based neuroanatomy, and discuss future directions in synaptic connectivity mapping and comparative connectomics.
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435
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Guo C, Pan Y, Gong Z. Recent Advances in the Genetic Dissection of Neural Circuits in Drosophila. Neurosci Bull 2019; 35:1058-1072. [PMID: 31119647 DOI: 10.1007/s12264-019-00390-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/17/2018] [Indexed: 11/28/2022] Open
Abstract
Nervous systems endow animals with cognition and behavior. To understand how nervous systems control behavior, neural circuits mediating distinct functions need to be identified and characterized. With superior genetic manipulability, Drosophila is a model organism at the leading edge of neural circuit analysis. We briefly introduce the state-of-the-art genetic tools that permit precise labeling of neurons and their interconnectivity and investigating what is happening in the brain of a behaving animal and manipulating neurons to determine how behaviors are affected. Brain-wide wiring diagrams, created by light and electron microscopy, bring neural circuit analysis to a new level and scale. Studies enabled by these tools advances our understanding of the nervous system in relation to cognition and behavior.
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Affiliation(s)
- Chao Guo
- Key Laboratory of Developmental Genes and Human Disease of the Ministry of Education of China, Institute of Life Sciences, Southeast University, Nanjing, 210096, China.
| | - Yufeng Pan
- Key Laboratory of Developmental Genes and Human Disease of the Ministry of Education of China, Institute of Life Sciences, Southeast University, Nanjing, 210096, China
| | - Zhefeng Gong
- Department of Neurobiology, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, Key Laboratory of Neurobiology, Zhejiang University School of Medicine, Hangzhou, 310058, China
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436
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Kobler JM, Grunwald Kadow IC. Flies spring a surprise. eLife 2019; 8:47720. [PMID: 31112128 PMCID: PMC6529215 DOI: 10.7554/elife.47720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/16/2019] [Indexed: 11/15/2022] Open
Abstract
A combination of genetic, anatomical and physiological techniques has revealed that the lateral horn, a region of the brain involved in olfaction in flies, has many more types of neurons than expected.
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Affiliation(s)
- Johanna M Kobler
- School of Life Sciences, Technical University of Munich, Munich, Germany.,Graduate School of Systemic Neuroscience (GSN), Ludwig-Maximilians-University, Munich, Germany
| | - Ilona C Grunwald Kadow
- School of Life Sciences, Technical University of Munich, Munich, Germany.,Graduate School of Systemic Neuroscience (GSN), Ludwig-Maximilians-University, Munich, Germany
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437
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Dolan MJ, Frechter S, Bates AS, Dan C, Huoviala P, Roberts RJV, Schlegel P, Dhawan S, Tabano R, Dionne H, Christoforou C, Close K, Sutcliffe B, Giuliani B, Li F, Costa M, Ihrke G, Meissner GW, Bock DD, Aso Y, Rubin GM, Jefferis GSXE. Neurogenetic dissection of the Drosophila lateral horn reveals major outputs, diverse behavioural functions, and interactions with the mushroom body. eLife 2019; 8:e43079. [PMID: 31112130 PMCID: PMC6529221 DOI: 10.7554/elife.43079] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/07/2019] [Indexed: 01/26/2023] Open
Abstract
Animals exhibit innate behaviours to a variety of sensory stimuli including olfactory cues. In Drosophila, one higher olfactory centre, the lateral horn (LH), is implicated in innate behaviour. However, our structural and functional understanding of the LH is scant, in large part due to a lack of sparse neurogenetic tools for this region. We generate a collection of split-GAL4 driver lines providing genetic access to 82 LH cell types. We use these to create an anatomical and neurotransmitter map of the LH and link this to EM connectomics data. We find ~30% of LH projections converge with outputs from the mushroom body, site of olfactory learning and memory. Using optogenetic activation, we identify LH cell types that drive changes in valence behavior or specific locomotor programs. In summary, we have generated a resource for manipulating and mapping LH neurons, providing new insights into the circuit basis of innate and learned olfactory behavior.
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Affiliation(s)
- Michael-John Dolan
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
- Division of NeurobiologyMRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Shahar Frechter
- Division of NeurobiologyMRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | | | - Chuntao Dan
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Paavo Huoviala
- Division of NeurobiologyMRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | | | - Philipp Schlegel
- Division of NeurobiologyMRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
- Department of ZoologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Serene Dhawan
- Division of NeurobiologyMRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
- Department of ZoologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Remy Tabano
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Heather Dionne
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | | | - Kari Close
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Ben Sutcliffe
- Division of NeurobiologyMRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Bianca Giuliani
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Feng Li
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Marta Costa
- Department of ZoologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Gudrun Ihrke
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | | | - Davi D Bock
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Yoshinori Aso
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Gerald M Rubin
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Gregory SXE Jefferis
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
- Division of NeurobiologyMRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
- Department of ZoologyUniversity of CambridgeCambridgeUnited Kingdom
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438
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Frechter S, Bates AS, Tootoonian S, Dolan MJ, Manton J, Jamasb AR, Kohl J, Bock D, Jefferis G. Functional and anatomical specificity in a higher olfactory centre. eLife 2019; 8:44590. [PMID: 31112127 PMCID: PMC6550879 DOI: 10.7554/elife.44590] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/12/2019] [Indexed: 12/16/2022] Open
Abstract
Most sensory systems are organized into parallel neuronal pathways that process distinct aspects of incoming stimuli. In the insect olfactory system, second order projection neurons target both the mushroom body, required for learning, and the lateral horn (LH), proposed to mediate innate olfactory behavior. Mushroom body neurons form a sparse olfactory population code, which is not stereotyped across animals. In contrast, odor coding in the LH remains poorly understood. We combine genetic driver lines, anatomical and functional criteria to show that the Drosophila LH has ~1400 neurons and >165 cell types. Genetically labeled LHNs have stereotyped odor responses across animals and on average respond to three times more odors than single projection neurons. LHNs are better odor categorizers than projection neurons, likely due to stereotyped pooling of related inputs. Our results reveal some of the principles by which a higher processing area can extract innate behavioral significance from sensory stimuli.
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Affiliation(s)
- Shahar Frechter
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Sina Tootoonian
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom.,Neurophysiology of Behaviour Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael-John Dolan
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Janelia Research Campus, Howard Hughes Medical Institute, Chevy Chase, United States
| | - James Manton
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Johannes Kohl
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Davi Bock
- Janelia Research Campus, Howard Hughes Medical Institute, Chevy Chase, United States
| | - Gregory Jefferis
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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439
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Hoffman C, Aballay A. Role of neurons in the control of immune defense. Curr Opin Immunol 2019; 60:30-36. [PMID: 31117013 DOI: 10.1016/j.coi.2019.04.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 11/28/2022]
Abstract
Studies in recent years have strengthened the notion that neural mechanisms are involved in the control of immune responses. From initial studies that highlighted the vagus nerve control of inflammatory responses in vertebrates, many advances have been made, including the dissection of specific neural circuits that are involved in controlling immunity. Part of this has been facilitated by the use of a tractable model animal, Caenorhabditis elegans, in which individual neurons involved in sensing pathogens and controlling the immune response have been identified. Importantly, some of the underlying mechanisms involved in the neural control of immune pathways appear to be present in evolutionarily diverse species. This review focuses on some major developments in vertebrates and C. elegans, and how these discoveries may lead to advances in understanding neural-immune connections that govern inflammatory responses.
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Affiliation(s)
- Casandra Hoffman
- Molecular Microbiology and Immunology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, 6351 Richard Jones Hall, Mail Code: L220, Portland, OR 97239, United States
| | - Alejandro Aballay
- Molecular Microbiology and Immunology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, 6351 Richard Jones Hall, Mail Code: L220, Portland, OR 97239, United States.
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440
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Lee K, Turner N, Macrina T, Wu J, Lu R, Seung HS. Convolutional nets for reconstructing neural circuits from brain images acquired by serial section electron microscopy. Curr Opin Neurobiol 2019; 55:188-198. [PMID: 31071619 DOI: 10.1016/j.conb.2019.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 04/05/2019] [Accepted: 04/10/2019] [Indexed: 11/30/2022]
Abstract
Neural circuits can be reconstructed from brain images acquired by serial section electron microscopy. Image analysis has been performed by manual labor for half a century, and efforts at automation date back almost as far. Convolutional nets were first applied to neuronal boundary detection a dozen years ago, and have now achieved impressive accuracy on clean images. Robust handling of image defects is a major outstanding challenge. Convolutional nets are also being employed for other tasks in neural circuit reconstruction: finding synapses and identifying synaptic partners, extending or pruning neuronal reconstructions, and aligning serial section images to create a 3D image stack. Computational systems are being engineered to handle petavoxel images of cubic millimeter brain volumes.
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Affiliation(s)
- Kisuk Lee
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Nicholas Turner
- Department of Computer Science, Princeton University, Princeton, NJ, 08544, USA
| | - Thomas Macrina
- Department of Computer Science, Princeton University, Princeton, NJ, 08544, USA
| | - Jingpeng Wu
- Neuroscience Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Ran Lu
- Neuroscience Institute, Princeton University, Princeton, NJ, 08544, USA
| | - H Sebastian Seung
- Department of Computer Science, Princeton University, Princeton, NJ, 08544, USA; Neuroscience Institute, Princeton University, Princeton, NJ, 08544, USA.
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441
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Big data in nanoscale connectomics, and the greed for training labels. Curr Opin Neurobiol 2019; 55:180-187. [PMID: 31055238 DOI: 10.1016/j.conb.2019.03.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 03/26/2019] [Accepted: 03/30/2019] [Indexed: 01/08/2023]
Abstract
The neurosciences have developed methods that outpace most other biomedical fields in terms of acquired bytes. We review how the information content and analysis challenge of such data indicates that electron microscopy (EM)-based connectomics is an especially hard problem. Here, as in many other current machine learning applications, the need for excessive amounts of labelled data while utilizing only a small fraction of available raw image data for algorithm training illustrates the still fundamental gap between artificial and biological intelligence. Substantial improvements of label and energy efficiency in machine learning may be required to address the formidable challenge of acquiring the nanoscale connectome of a human brain.
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442
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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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443
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Hsu KJ, Lin YY, Chiang AS, Chu SW. Optical properties of adult Drosophila brains in one-, two-, and three-photon microscopy. BIOMEDICAL OPTICS EXPRESS 2019; 10:1627-1637. [PMID: 31086697 PMCID: PMC6484994 DOI: 10.1364/boe.10.001627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/23/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
Drosophila is widely used in connectome studies due to its small brain size, sophisticated genetic tools, and the most complete single-neuron-based anatomical brain map. Surprisingly, even the brain thickness is only 200-μm, common Ti:sapphire-based two-photon excitation cannot penetrate, possibly due to light aberration/scattering of trachea. Here we quantitatively characterized scattering and light distortion of trachea-filled tissues, and found that trachea-induced light distortion dominates at long wavelength by comparing one-photon (488-nm), two-photon (920-nm), and three-photon (1300-nm) excitations. Whole-Drosophila-brain imaging is achieved by reducing tracheal light aberration/scattering via brain-degassing or long-wavelength excitation at 1300-nm. Our work paves the way toward constructing whole-brain connectome in a living Drosophila.
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Affiliation(s)
- Kuo-Jen Hsu
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yen-Yin Lin
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ann-Shyn Chiang
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu 30013, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80780, Taiwan
- Kavli Institute for Brain and Mind, University of California at San Diego, La Jolla, CA 92093-0526, USA
| | - Shi-Wei Chu
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
- Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
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444
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Corrigendum to “Progress and remaining challenges in high-throughput volume electron microscopy” [Curr Opin Neurobiol 50 (June 2018) 261-267]. Curr Opin Neurobiol 2019; 55:213. [DOI: 10.1016/j.conb.2019.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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445
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Caffrey BJ, Maltsev AV, Gonzalez-Freire M, Hartnell LM, Ferrucci L, Subramaniam S. Semi-automated 3D segmentation of human skeletal muscle using Focused Ion Beam-Scanning Electron Microscopic images. J Struct Biol 2019; 207:1-11. [PMID: 30914296 DOI: 10.1016/j.jsb.2019.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 12/11/2022]
Abstract
Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) is an imaging approach that enables analysis of the 3D architecture of cells and tissues at resolutions that are 1-2 orders of magnitude higher than that possible with light microscopy. The slow speeds of data collection and manual segmentation are two critical problems that limit the more extensive use of FIB-SEM technology. Here, we present an easily accessible robust method that enables rapid, large-scale acquisition of data from tissue specimens, combined with an approach for semi-automated data segmentation using the open-source machine learning Weka segmentation software, which dramatically increases the speed of image analysis. We demonstrate the feasibility of these methods through the 3D analysis of human muscle tissue by showing that our process results in an improvement in speed of up to three orders of magnitude as compared to manual approaches for data segmentation. All programs and scripts we use are open source and are immediately available for use by others.
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Affiliation(s)
| | - Alexander V Maltsev
- Longitudinal Studies Section, National Institute on Aging, National Institutes of Health, Baltimore, MD 21225, USA
| | - Marta Gonzalez-Freire
- Longitudinal Studies Section, National Institute on Aging, National Institutes of Health, Baltimore, MD 21225, USA
| | - Lisa M Hartnell
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, National Institute on Aging, National Institutes of Health, Baltimore, MD 21225, USA.
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446
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Zhang Q, Lee WCA, Paul DL, Ginty DD. Multiplexed peroxidase-based electron microscopy labeling enables simultaneous visualization of multiple cell types. Nat Neurosci 2019; 22:828-839. [PMID: 30886406 PMCID: PMC6555422 DOI: 10.1038/s41593-019-0358-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/07/2019] [Indexed: 01/06/2023]
Abstract
Electron microscopy (EM) is a powerful tool for circuit mapping, but identifying specific cell types in EM datasets remains a major challenge. Here we describe a technique enabling simultaneous visualization of multiple, genetically identified neuronal populations so that synaptic interactions between them can be unequivocally defined. We present 15 AAV constructs and six mouse reporter lines for multiplexed EM labeling in the mammalian nervous system. These reporters feature dAPEX2, which exhibits dramatically improved signal compared to previously described ascorbate peroxidases. By targeting this enhanced peroxidase to different subcellular compartments, multiple orthogonal reporters can be simultaneously visualized and distinguished under EM using a protocol compatible with existing EM pipelines. Proof-of-principle double and triple EM labeling experiments demonstrated synaptic connections between primary afferents, descending cortical inputs, and inhibitory interneurons in the spinal cord dorsal horn. Our multiplexed peroxidase-based EM labeling system should therefore greatly facilitate analysis of connectivity in the nervous system.
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Affiliation(s)
- Qiyu Zhang
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Wei-Chung A Lee
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - David L Paul
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
| | - David D Ginty
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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447
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Ache JM, Polsky J, Alghailani S, Parekh R, Breads P, Peek MY, Bock DD, von Reyn CR, Card GM. Neural Basis for Looming Size and Velocity Encoding in the Drosophila Giant Fiber Escape Pathway. Curr Biol 2019; 29:1073-1081.e4. [DOI: 10.1016/j.cub.2019.01.079] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/18/2019] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
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448
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Venkatasubramanian L, Mann RS. The development and assembly of the Drosophila adult ventral nerve cord. Curr Opin Neurobiol 2019; 56:135-143. [PMID: 30826502 DOI: 10.1016/j.conb.2019.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 01/05/2023]
Abstract
In order to generate complex motor outputs, the nervous system integrates multiple sources of sensory information that ultimately controls motor neurons to generate coordinated movements. The neural circuits that integrate higher order commands from the brain and generate motor outputs are located in the nerve cord of the central nervous system. Recently, genetic access to distinct functional subtypes that make up the Drosophila adult ventral nerve cord has significantly begun to advance our understanding of the structural organization and functions of the neural circuits coordinating motor outputs. Moreover, lineage-tracing and genetic intersection tools have been instrumental in deciphering the developmental mechanisms that generate and assemble the functional units of the adult nerve cord. Together, the Drosophila adult ventral nerve cord is emerging as a powerful system to understand the development and function of neural circuits that are responsible for coordinating complex motor outputs.
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Affiliation(s)
- Lalanti Venkatasubramanian
- Department of Biochemistry and Molecular Biophysics, Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, United States
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, United States.
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449
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Deng B, Li Q, Liu X, Cao Y, Li B, Qian Y, Xu R, Mao R, Zhou E, Zhang W, Huang J, Rao Y. Chemoconnectomics: Mapping Chemical Transmission in Drosophila. Neuron 2019; 101:876-893.e4. [PMID: 30799021 DOI: 10.1016/j.neuron.2019.01.045] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 11/02/2018] [Accepted: 01/17/2019] [Indexed: 12/27/2022]
Abstract
We define the chemoconnectome (CCT) as the entire set of neurotransmitters, neuromodulators, neuropeptides, and their receptors underlying chemotransmission in an animal. We have generated knockout lines of Drosophila CCT genes for functional investigations and knockin lines containing Gal4 and other tools for examining gene expression and manipulating neuronal activities, with a versatile platform allowing genetic intersections and logic gates. CCT reveals the coexistence of specific transmitters but mutual exclusion of the major inhibitory and excitatory transmitters in the same neurons. One neuropeptide and five receptors were detected in glia, with octopamine β2 receptor functioning in glia. A pilot screen implicated 41 genes in sleep regulation, with the dopamine receptor Dop2R functioning in neurons expressing the peptides Dilp2 and SIFa. Thus, CCT is a novel concept, chemoconnectomics a new approach, and CCT tool lines a powerful resource for systematic investigations of chemical-transmission-mediated neural signaling circuits underlying behavior and cognition.
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Affiliation(s)
- Bowen Deng
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Advanced Innovation Center for Genomics, Peking University School of Life Sciences, Chinese Institute for Brain Research, Beijing, Zhongguangchun Life Sciences Park, Beijing, China
| | - Qi Li
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Advanced Innovation Center for Genomics, Peking University School of Life Sciences, Chinese Institute for Brain Research, Beijing, Zhongguangchun Life Sciences Park, Beijing, China
| | - Xinxing Liu
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Advanced Innovation Center for Genomics, Peking University School of Life Sciences, Chinese Institute for Brain Research, Beijing, Zhongguangchun Life Sciences Park, Beijing, China
| | - Yue Cao
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Advanced Innovation Center for Genomics, Peking University School of Life Sciences, Chinese Institute for Brain Research, Beijing, Zhongguangchun Life Sciences Park, Beijing, China
| | - Bingfeng Li
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Advanced Innovation Center for Genomics, Peking University School of Life Sciences, Chinese Institute for Brain Research, Beijing, Zhongguangchun Life Sciences Park, Beijing, China
| | - Yongjun Qian
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Advanced Innovation Center for Genomics, Peking University School of Life Sciences, Chinese Institute for Brain Research, Beijing, Zhongguangchun Life Sciences Park, Beijing, China
| | - Rui Xu
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Renbo Mao
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Advanced Innovation Center for Genomics, Peking University School of Life Sciences, Chinese Institute for Brain Research, Beijing, Zhongguangchun Life Sciences Park, Beijing, China
| | - Enxing Zhou
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Advanced Innovation Center for Genomics, Peking University School of Life Sciences, Chinese Institute for Brain Research, Beijing, Zhongguangchun Life Sciences Park, Beijing, China
| | - Wenxia Zhang
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Advanced Innovation Center for Genomics, Peking University School of Life Sciences, Chinese Institute for Brain Research, Beijing, Zhongguangchun Life Sciences Park, Beijing, China
| | - Juan Huang
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yi Rao
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Advanced Innovation Center for Genomics, Peking University School of Life Sciences, Chinese Institute for Brain Research, Beijing, Zhongguangchun Life Sciences Park, Beijing, China.
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Baker CA, Clemens J, Murthy M. Acoustic Pattern Recognition and Courtship Songs: Insights from Insects. Annu Rev Neurosci 2019; 42:129-147. [PMID: 30786225 DOI: 10.1146/annurev-neuro-080317-061839] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Across the animal kingdom, social interactions rely on sound production and perception. From simple cricket chirps to more elaborate bird songs, animals go to great lengths to communicate information critical for reproduction and survival via acoustic signals. Insects produce a wide array of songs to attract a mate, and the intended receivers must differentiate these calls from competing sounds, analyze the quality of the sender from spectrotemporal signal properties, and then determine how to react. Insects use numerically simple nervous systems to analyze and respond to courtship songs, making them ideal model systems for uncovering the neural mechanisms underlying acoustic pattern recognition. We highlight here how the combination of behavioral studies and neural recordings in three groups of insects-crickets, grasshoppers, and fruit flies-reveals common strategies for extracting ethologically relevant information from acoustic patterns and how these findings might translate to other systems.
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Affiliation(s)
- Christa A Baker
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey 08544, USA;
| | - Jan Clemens
- University Medical Center Goettingen, Max-Planck-Society, European Neuroscience Institute, D-37077 Goettingen, Germany;
| | - Mala Murthy
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey 08544, USA;
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