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Jaiswal A, Boring A, Mukherjee A, Avidor-Reiss T. Fly Fam161 is an essential centriole and cilium transition zone protein with unique and diverse cell type-specific localizations. Open Biol 2024; 14:240036. [PMID: 39255847 PMCID: PMC11500687 DOI: 10.1098/rsob.240036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/17/2024] [Accepted: 07/15/2024] [Indexed: 09/12/2024] Open
Abstract
Family with sequence similarity 161 (Fam161) is an ancient family of microtubule-binding proteins located at the centriole and cilium transition zone (TZ) lumen that exhibit rapid evolution in mice. However, their adaptive role is unclear. Here, we used flies to gain insight into their cell type-specific adaptations. Fam161 is the sole orthologue of FAM161A and FAM161B found in flies. Mutating Fam161 results in reduced male reproduction and abnormal geotaxis behaviour. Fam161 localizes to sensory neuron centrioles and their specialized TZ (the connecting cilium) in a cell type-specific manner, sometimes labelling only the centrioles, sometimes labelling the centrioles and cilium TZ and sometimes labelling the TZ with varying lengths that are longer than other TZ proteins, defining a new ciliary compartment, the extra distal TZ. These findings suggest that Fam161 is an essential centriole and TZ protein with a unique cell type-specific localization in fruit flies that can produce cell type-specific adaptations.
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Affiliation(s)
- Ankit Jaiswal
- Department of Biological Sciences, University of Toledo, Toledo, OH43606, USA
| | - Andrew Boring
- Department of Biological Sciences, University of Toledo, Toledo, OH43606, USA
- Department of Urology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH43614, USA
| | - Avik Mukherjee
- Department of Biological Sciences, University of Toledo, Toledo, OH43606, USA
| | - Tomer Avidor-Reiss
- Department of Biological Sciences, University of Toledo, Toledo, OH43606, USA
- Department of Urology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH43614, USA
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2
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Sun L, Meissner J, He J, Cui L, Fürstenhaupt T, Liang X. Resolving the In Situ Three-Dimensional Structure of Fly Mechanosensory Organelles Using Serial Section Electron Tomography. Bio Protoc 2024; 14:e4940. [PMID: 38405077 PMCID: PMC10883892 DOI: 10.21769/bioprotoc.4940] [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: 11/20/2023] [Revised: 12/29/2023] [Accepted: 01/17/2024] [Indexed: 02/27/2024] Open
Abstract
Mechanosensory organelles (MOs) are specialized subcellular entities where force-sensitive channels and supporting structures (e.g., microtubule cytoskeleton) are organized in an orderly manner. The delicate structure of MOs needs to be resolved to understand the mechanisms by which they detect forces and how they are formed. Here, we describe a protocol that allows obtaining detailed information about the nanoscopic ultrastructure of fly MOs by using serial section electron tomography (SS-ET). To preserve fine structural details, the tissues are cryo-immobilized using a high-pressure freezer followed by freeze-substitution at low temperature and embedding in resin at room temperature. Then, sample sections are prepared and used to acquire the dual-axis tilt series images, which are further processed for tomographic reconstruction. Finally, tomograms of consecutive sections are combined into a single larger volume using microtubules as fiducial markers. Using this protocol, we managed to reconstruct the sensory organelles, which provide novel molecular insights as to how fly mechanosensory organelles work and are formed. Based on our experience, we think that, with minimal modifications, this protocol can be adapted to a wide range of applications using different cell and tissue samples. Key features • Resolving the high-resolution 3D ultrastructure of subcellular organelles using serial section electron tomography (SS-ET). • Compared with single-axis tilt series, dual-axis tilt series provides a much wider coverage of Fourier space, improving resolution and features in the reconstructed tomograms. • The use of high-pressure freezing and freeze-substitution maximally preserves the fine structural details.
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Affiliation(s)
- Landi Sun
- IDG/McGovern Institute for Brain Research, School of
Life Sciences, Tsinghua University, Beijing, China
- Guangzhou National Laboratory, Guangzhou, China
| | - Jana Meissner
- Electron Microscopy Facility, Max Planck Institute of
Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jianfeng He
- IDG/McGovern Institute for Brain Research, School of
Life Sciences, Tsinghua University, Beijing, China
| | - Lihong Cui
- Center of Biomedical Analysis, School of Life
Sciences, Tsinghua University, Beijing, China
| | - Tobias Fürstenhaupt
- Electron Microscopy Facility, Max Planck Institute of
Molecular Cell Biology and Genetics, Dresden, Germany
| | - Xin Liang
- IDG/McGovern Institute for Brain Research, School of
Life Sciences, Tsinghua University, Beijing, China
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3
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Boyan G, Williams L, Ehrhardt E. Central projections from Johnston's organ in the locust: Axogenesis and brain neuroarchitecture. Dev Genes Evol 2023; 233:147-159. [PMID: 37695323 PMCID: PMC10746777 DOI: 10.1007/s00427-023-00710-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023]
Abstract
Johnston's organ (Jo) acts as an antennal wind-sensitive and/or auditory organ across a spectrum of insect species and its axons universally project to the brain. In the locust, this pathway is already present at mid-embryogenesis but the process of fasciculation involved in its construction has not been investigated. Terminal projections into the fine neuropilar organization of the brain also remain unresolved, information essential not only for understanding the neural circuitry mediating Jo-mediated behavior but also for providing comparative data offering insights into its evolution. In our study here, we employ neuron-specific, axon-specific, and epithelial domain labels to show that the pathway to the brain of the locust is built in a stepwise manner during early embryogenesis as processes from Jo cell clusters in the pedicel fasciculate first with one another, and then with the two tracts constituting the pioneer axon scaffold of the antenna. A comparison of fasciculation patterns confirms that projections from cell clusters of Jo stereotypically associate with only one axon tract according to their location in the pedicellar epithelium, consistent with a topographic plan. At the molecular level, all neuronal elements of the Jo pathway to the brain express the lipocalin Lazarillo, a cell surface epitope that regulates axogenesis in the primary axon scaffold itself, and putatively during fasciculation of the Jo projections to the brain. Central projections from Jo first contact the primary axon scaffold of the deutocerebral brain at mid-embryogenesis, and in the adult traverse mechanosensory/motor neuropils similar to those in Drosophila. These axons then terminate among protocerebral commissures containing premotor interneurons known to regulate flight behavior.
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Affiliation(s)
- George Boyan
- Graduate School of Systemic Neuroscience, Biocenter, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152, Munich, Planegg-Martinsried, Germany.
| | - Leslie Williams
- Graduate School of Systemic Neuroscience, Biocenter, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152, Munich, Planegg-Martinsried, Germany
| | - Erica Ehrhardt
- Graduate School of Systemic Neuroscience, Biocenter, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152, Munich, Planegg-Martinsried, Germany
- Institute of Zoology, AG Ito, Universität Zu Köln, Zülpicher Str. 47B, 50674, Cologne, Germany
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4
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Mitchell JW, Midillioglu I, Schauer E, Wang B, Han C, Wildonger J. Coordination of Pickpocket ion channel delivery and dendrite growth in Drosophila sensory neurons. PLoS Genet 2023; 19:e1011025. [PMID: 37943859 PMCID: PMC10662761 DOI: 10.1371/journal.pgen.1011025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/21/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
Sensory neurons enable an organism to perceive external stimuli, which is essential for survival. The sensory capacity of a neuron depends on the elaboration of its dendritic arbor and the localization of sensory ion channels to the dendritic membrane. However, it is not well understood when and how ion channels localize to growing sensory dendrites and whether their delivery is coordinated with growth of the dendritic arbor. We investigated the localization of the DEG/ENaC/ASIC ion channel Pickpocket (Ppk) in the peripheral sensory neurons of developing fruit flies. We used CRISPR-Cas9 genome engineering approaches to tag endogenous Ppk1 and visualize it live, including monitoring Ppk1 membrane localization via a novel secreted split-GFP approach. Fluorescently tagged endogenous Ppk1 localizes to dendrites, as previously reported, and, unexpectedly, to axons and axon terminals. In dendrites, Ppk1 is present throughout actively growing dendrite branches and is stably integrated into the neuronal cell membrane during the expansive growth of the arbor. Although Ppk channels are dispensable for dendrite growth, we found that an over-active channel mutant severely reduces dendrite growth, likely by acting at an internal membrane and not the dendritic membrane. Our data reveal that the molecular motor dynein and recycling endosome GTPase Rab11 are needed for the proper trafficking of Ppk1 to dendrites. Based on our data, we propose that Ppk channel transport is coordinated with dendrite morphogenesis, which ensures proper ion channel density and distribution in sensory dendrites.
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Affiliation(s)
- Josephine W. Mitchell
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Chemistry and Biochemistry, Kalamazoo College, Kalamazoo, Michigan, United States of America
| | - Ipek Midillioglu
- Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Ethan Schauer
- Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Bei Wang
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Chun Han
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Jill Wildonger
- Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- Cell & Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
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5
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Kohsaka H. Linking neural circuits to the mechanics of animal behavior in Drosophila larval locomotion. Front Neural Circuits 2023; 17:1175899. [PMID: 37711343 PMCID: PMC10499525 DOI: 10.3389/fncir.2023.1175899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/13/2023] [Indexed: 09/16/2023] Open
Abstract
The motions that make up animal behavior arise from the interplay between neural circuits and the mechanical parts of the body. Therefore, in order to comprehend the operational mechanisms governing behavior, it is essential to examine not only the underlying neural network but also the mechanical characteristics of the animal's body. The locomotor system of fly larvae serves as an ideal model for pursuing this integrative approach. By virtue of diverse investigation methods encompassing connectomics analysis and quantification of locomotion kinematics, research on larval locomotion has shed light on the underlying mechanisms of animal behavior. These studies have elucidated the roles of interneurons in coordinating muscle activities within and between segments, as well as the neural circuits responsible for exploration. This review aims to provide an overview of recent research on the neuromechanics of animal locomotion in fly larvae. We also briefly review interspecific diversity in fly larval locomotion and explore the latest advancements in soft robots inspired by larval locomotion. The integrative analysis of animal behavior using fly larvae could establish a practical framework for scrutinizing the behavior of other animal species.
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Affiliation(s)
- Hiroshi Kohsaka
- Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo, Japan
- Department of Complexity Science and Engineering, Graduate School of Frontier Science, The University of Tokyo, Chiba, Japan
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6
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Ravenscroft TA, Jacobs A, Gu M, Eberl DF, Bellen HJ. The Voltage-Gated Sodium Channel in Drosophila, Para, Localizes to Dendrites As Well As Axons in Mechanosensitive Chordotonal Neurons. eNeuro 2023; 10:ENEURO.0105-23.2023. [PMID: 37328295 PMCID: PMC10316460 DOI: 10.1523/eneuro.0105-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/12/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023] Open
Abstract
The fruit fly Drosophila melanogaster has provided important insights into how sensory information is transduced by transient receptor potential (TRP) channels in the peripheral nervous system (PNS). However, TRP channels alone have not been able to completely model mechanosensitive transduction in mechanoreceptive chordotonal neurons (CNs). Here, we show that, in addition to TRP channels, the sole voltage-gated sodium channel (NaV) in Drosophila, Para, is localized to the dendrites of CNs. Para is localized to the distal tip of the dendrites in all CNs, from embryos to adults, and is colocalized with the mechanosensitive TRP channels No mechanoreceptor potential C (NompC) and Inactive/Nanchung (Iav/Nan). Para localization also demarcates spike initiation zones (SIZs) in axons and the dendritic localization of Para is indicative of a likely dendritic SIZ in fly CNs. Para is not present in the dendrites of other peripheral sensory neurons. In both multipolar and bipolar neurons in the PNS, Para is present in a proximal region of the axon, comparable to the axonal initial segment (AIS) in vertebrates, 40-60 μm from the soma in multipolar neurons and 20-40 μm in bipolar neurons. Whole-cell reduction of para expression using RNAi in CNs of the adult Johnston's organ (JO) severely affects sound-evoked potentials (SEPs). However, the duality of Para localization in the CN dendrites and axons identifies a need to develop resources to study compartment-specific roles of proteins that will enable us to better understand Para's role in mechanosensitive transduction.
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Affiliation(s)
- Thomas A Ravenscroft
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030
- Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030
| | - Ashleigh Jacobs
- Department of Biology, University of Iowa, Iowa City, IA 52242
| | - Mingxue Gu
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030
- Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030
| | - Daniel F Eberl
- Department of Biology, University of Iowa, Iowa City, IA 52242
| | - Hugo J Bellen
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030
- Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
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7
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Boivin JC, Zhu J, Ohyama T. Nociception in fruit fly larvae. FRONTIERS IN PAIN RESEARCH 2023; 4:1076017. [PMID: 37006412 PMCID: PMC10063880 DOI: 10.3389/fpain.2023.1076017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
Nociception, the process of encoding and processing noxious or painful stimuli, allows animals to detect and avoid or escape from potentially life-threatening stimuli. Here, we provide a brief overview of recent technical developments and studies that have advanced our understanding of the Drosophila larval nociceptive circuit and demonstrated its potential as a model system to elucidate the mechanistic basis of nociception. The nervous system of a Drosophila larva contains roughly 15,000 neurons, which allows for reconstructing the connectivity among them directly by transmission electron microscopy. In addition, the availability of genetic tools for manipulating the activity of individual neurons and recent advances in computational and high-throughput behavior analysis methods have facilitated the identification of a neural circuit underlying a characteristic nocifensive behavior. We also discuss how neuromodulators may play a key role in modulating the nociceptive circuit and behavioral output. A detailed understanding of the structure and function of Drosophila larval nociceptive neural circuit could provide insights into the organization and operation of pain circuits in mammals and generate new knowledge to advance the development of treatment options for pain in humans.
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Affiliation(s)
- Jean-Christophe Boivin
- Department of Biology, McGill University, Montreal, QC, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
| | - Jiayi Zhu
- Department of Biology, McGill University, Montreal, QC, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
| | - Tomoko Ohyama
- Department of Biology, McGill University, Montreal, QC, Canada
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
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8
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Banka S, Bennington A, Baker MJ, Rijckmans E, Clemente GD, Ansor NM, Sito H, Prasad P, Anyane-Yeboa K, Badalato L, Dimitrov B, Fitzpatrick D, Hurst ACE, Jansen AC, Kelly MA, Krantz I, Rieubland C, Ross M, Rudy NL, Sanz J, Stouffs K, Xu ZL, Malliri A, Kazanietz MG, Millard TH. Activating RAC1 variants in the switch II region cause a developmental syndrome and alter neuronal morphology. Brain 2022; 145:4232-4245. [PMID: 35139179 PMCID: PMC9762944 DOI: 10.1093/brain/awac049] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 11/14/2022] Open
Abstract
RAC1 is a highly conserved Rho GTPase critical for many cellular and developmental processes. De novo missense RAC1 variants cause a highly variable neurodevelopmental disorder. Some of these variants have previously been shown to have a dominant negative effect. Most previously reported patients with this disorder have either severe microcephaly or severe macrocephaly. Here, we describe eight patients with pathogenic missense RAC1 variants affecting residues between Q61 and R68 within the switch II region of RAC1. These patients display variable combinations of developmental delay, intellectual disability, brain anomalies such as polymicrogyria and cardiovascular defects with normocephaly or relatively milder micro- or macrocephaly. Pulldown assays, NIH3T3 fibroblast spreading assays and staining for activated PAK1/2/3 and WAVE2 suggest that these variants increase RAC1 activity and over-activate downstream signalling targets. Axons of neurons isolated from Drosophila embryos expressing the most common of the activating variants are significantly shorter, with an increased density of filopodial protrusions. In vivo, these embryos exhibit frequent defects in axonal organization. Class IV dendritic arborization neurons expressing this variant exhibit a significant reduction in the total area of the dendritic arbour, increased branching and failure of self-avoidance. RNAi knock down of the WAVE regulatory complex component Cyfip significantly rescues these morphological defects. These results establish that activating substitutions affecting residues Q61-R68 within the switch II region of RAC1 cause a developmental syndrome. Our findings reveal that these variants cause altered downstream signalling, resulting in abnormal neuronal morphology and reveal the WAVE regulatory complex/Arp2/3 pathway as a possible therapeutic target for activating RAC1 variants. These insights also have the potential to inform the mechanism and therapy for other disorders caused by variants in genes encoding other Rho GTPases, their regulators and downstream effectors.
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Affiliation(s)
- Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Manchester Centre for Genomic Medicine, University of Manchester, St Mary’s Hospital, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Abigail Bennington
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, University of ManchesterM13 9PL, UK
| | - Martin J Baker
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell Signalling Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield SK10 4TG, UK
| | - Ellen Rijckmans
- Department of Pediatrics, UZ Brussel, Brussels, Belgium
- Neurogenetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Giuliana D Clemente
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, University of ManchesterM13 9PL, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Nurhuda Mohamad Ansor
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, University of ManchesterM13 9PL, UK
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Penang, Malaysia
| | - Hilary Sito
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, University of ManchesterM13 9PL, UK
| | - Pritha Prasad
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, University of ManchesterM13 9PL, UK
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Columbia University Medical Center, New York 10032, USA
| | - Lauren Badalato
- Department of Pediatrics, School of Medicine, Kingston General Hospital, Queen’s University, Kingston, ON, Canada
| | - Boyan Dimitrov
- Centre for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - David Fitzpatrick
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anna C Jansen
- Neurogenetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
- Pediatric Neurology Unit, Department of Pediatrics, UZ Brussel, Brussels, Belgium
| | | | - Ian Krantz
- Roberts Individualized Medical Genetics Center, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Claudine Rieubland
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Meredith Ross
- Division of Clinical Genetics, Columbia University Medical Center, New York 10032, USA
| | - Natasha L Rudy
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Javier Sanz
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Katrien Stouffs
- Neurogenetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
- Centre for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Zhuo Luan Xu
- Roberts Individualized Medical Genetics Center, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Angeliki Malliri
- Cell Signalling Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield SK10 4TG, UK
| | - Marcelo G Kazanietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tom H Millard
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, University of ManchesterM13 9PL, UK
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9
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Boyan G, Ehrhardt E. Early embryonic development of Johnston's organ in the antenna of the desert locust Schistocerca gregaria. Dev Genes Evol 2022; 232:103-113. [PMID: 36138225 PMCID: PMC9691482 DOI: 10.1007/s00427-022-00695-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/13/2022] [Indexed: 01/30/2023]
Abstract
Johnston's organ has been shown to act as an antennal auditory organ across a spectrum of insect species. In the hemimetabolous desert locust Schistocerca gregaria, Johnston's organ must be functional on hatching and so develops in the pedicellar segment of the antenna during embryogenesis. Here, we employ the epithelial cell marker Lachesin to identify the pedicellar domain of the early embryonic antenna and then triple-label against Lachesin, the mitosis marker phosphohistone-3, and neuron-specific horseradish peroxidase to reveal the sense-organ precursors for Johnston's organ and their lineages. Beginning with a single progenitor at approximately a third of embryogenesis, additional precursors subsequently appear in both the ventral and dorsal pedicellar domains, each generating a lineage or clone. Lineage locations are remarkably conserved across preparations and ages, consistent with the epithelium possessing an underlying topographic coordinate system that determines the cellular organization of Johnston's organ. By mid-embryogenesis, twelve lineages are arranged circumferentially in the pedicel as in the adult structure. Each sense-organ precursor is associated with a smaller mitotically active cell from which the neuronal complement of each clone may derive. Neuron numbers within a clone increase in discrete steps with age and are invariant between clones and across preparations of a given age. At mid-embryogenesis, each clone comprises five cells consolidated into a tightly bound cartridge. A long scolopale extends apically from each cartridge to an insertion point in the epithelium, and bundled axons project basally toward the brain. Comparative data suggest mechanisms that might also regulate the developmental program of Johnston's organ in the locust.
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Affiliation(s)
- George Boyan
- Graduate School of Systemic Neuroscience, Biocenter, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152, Munich, Planegg-Martinsried, Germany.
| | - Erica Ehrhardt
- Graduate School of Systemic Neuroscience, Biocenter, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152, Munich, Planegg-Martinsried, Germany
- Institute of Zoology, Universität Zu Köln, Zülpicher Str. 47b, 50674, Cologne, Germany
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10
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Liu C, Zhang W. Molecular basis of somatosensation in insects. Curr Opin Neurobiol 2022; 76:102592. [DOI: 10.1016/j.conb.2022.102592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]
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11
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Shin GJE, Abaci HE, Smith MC. Cellular Pathogenesis of Chemotherapy-Induced Peripheral Neuropathy: Insights From Drosophila and Human-Engineered Skin Models. FRONTIERS IN PAIN RESEARCH 2022; 3:912977. [PMID: 35875478 PMCID: PMC9304629 DOI: 10.3389/fpain.2022.912977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Chemotherapy-induced peripheral neuropathy (CIPN) is a highly prevalent and complex condition arising from chemotherapy cancer treatments. Currently, there are no treatment or prevention options in the clinic. CIPN accompanies pain-related sensory functions starting from the hands and feet. Studies focusing on neurons in vitro and in vivo models significantly advanced our understanding of CIPN pathological mechanisms. However, given the direct toxicity shown in both neurons and non-neuronal cells, effective in vivo or in vitro models that allow the investigation of neurons in their local environment are required. No single model can provide a complete solution for the required investigation, therefore, utilizing a multi-model approach would allow complementary advantages of different models and robustly validate findings before further translation. This review aims first to summarize approaches and insights from CIPN in vivo models utilizing small model organisms. We will focus on Drosophila melanogaster CIPN models that are genetically amenable and accessible to study neuronal interactions with the local environment in vivo. Second, we will discuss how these findings could be tested in physiologically relevant vertebrate models. We will focus on in vitro approaches using human cells and summarize the current understanding of engineering approaches that may allow the investigation of pathological changes in neurons and the skin environment.
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Affiliation(s)
- Grace Ji-eun Shin
- Zuckerman Mind Brain and Behavior Institute, Jerome L. Greene Science Center, Columbia University, New York, NY, United States
- *Correspondence: Grace Ji-eun Shin
| | - Hasan Erbil Abaci
- Department of Dermatology, Columbia University Medical Center, Saint Nicholas Avenue, New York, NY, United States
| | - Madison Christine Smith
- Zuckerman Mind Brain and Behavior Institute, Jerome L. Greene Science Center, Columbia University, New York, NY, United States
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12
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Shree S, Sutradhar S, Trottier O, Tu Y, Liang X, Howard J. Dynamic instability of dendrite tips generates the highly branched morphologies of sensory neurons. SCIENCE ADVANCES 2022; 8:eabn0080. [PMID: 35767611 PMCID: PMC9242452 DOI: 10.1126/sciadv.abn0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The highly ramified arbors of neuronal dendrites provide the substrate for the high connectivity and computational power of the brain. Altered dendritic morphology is associated with neuronal diseases. Many molecules have been shown to play crucial roles in shaping and maintaining dendrite morphology. However, the underlying principles by which molecular interactions generate branched morphologies are not understood. To elucidate these principles, we visualized the growth of dendrites throughout larval development of Drosophila sensory neurons and found that the tips of dendrites undergo dynamic instability, transitioning rapidly and stochastically between growing, shrinking, and paused states. By incorporating these measured dynamics into an agent-based computational model, we showed that the complex and highly variable dendritic morphologies of these cells are a consequence of the stochastic dynamics of their dendrite tips. These principles may generalize to branching of other neuronal cell types, as well as to branching at the subcellular and tissue levels.
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Affiliation(s)
- Sonal Shree
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Sabyasachi Sutradhar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Olivier Trottier
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Department of Physics, Yale University, New Haven, CT 06511, USA
| | - Yuhai Tu
- IBM T.J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Xin Liang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jonathon Howard
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Department of Physics, Yale University, New Haven, CT 06511, USA
- Quantitative Biology Institute, Yale University, New Haven, CT 06511, USA
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13
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Colon-Plaza S, Su TT. Non-Apoptotic Role of Apoptotic Caspases in the Drosophila Nervous System. Front Cell Dev Biol 2022; 10:839358. [PMID: 35223857 PMCID: PMC8863954 DOI: 10.3389/fcell.2022.839358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 01/14/2022] [Indexed: 01/11/2023] Open
Abstract
An increasing number of studies demonstrate that cells can activate apoptotic caspases but not die and, instead, display profound changes in cellular structure and function. In this minireview, we will discuss observations in the nervous system of Drosophila melanogaster that illustrate non-apoptotic roles of apoptotic caspases. We will preface these examples with similar observations in other experimental systems and end with a discussion of how apoptotic caspase activity might be constrained to provide non-lethal functions without killing the cell.
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Affiliation(s)
- Sarah Colon-Plaza
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, United States
| | - Tin Tin Su
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, United States
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14
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Ormerod KG, Scibelli AE, Littleton JT. Regulation of excitation-contraction coupling at the Drosophila neuromuscular junction. J Physiol 2022; 600:349-372. [PMID: 34788476 PMCID: PMC9044916 DOI: 10.1113/jp282092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/28/2021] [Indexed: 01/05/2023] Open
Abstract
The Drosophila neuromuscular system is widely used to characterize synaptic development and function. However, little is known about how specific synaptic alterations effect neuromuscular transduction and muscle contractility, which ultimately dictate behavioural output. Here we develop and use a force transducer system to characterize excitation-contraction coupling at Drosophila larval neuromuscular junctions (NMJs), examining how specific neuronal and muscle manipulations disrupt muscle contractility. Muscle contraction force increased with motoneuron stimulation frequency and duration, showing considerable plasticity between 5 and 40 Hz and saturating above 50 Hz. Endogenous recordings of fictive contractions revealed average motoneuron burst frequencies of 20-30 Hz, consistent with the system operating within this plastic range of contractility. Temperature was also a key factor in muscle contractility, as force was enhanced at lower temperatures and dramatically reduced with increasing temperatures. Pharmacological and genetic manipulations of critical components of Ca2+ regulation in both pre- and postsynaptic compartments affected the strength and time course of muscle contractions. A screen for modulators of muscle contractility led to identification and characterization of the molecular and cellular pathway by which the FMRFa peptide, TPAEDFMRFa, increases muscle performance. These findings indicate Drosophila NMJs provide a robust system to correlate synaptic dysfunction, regulation and modulation to alterations in excitation-contraction coupling. KEY POINTS: Larval muscle contraction force increases with stimulation frequency and duration, revealing substantial plasticity between 5 and 40 Hz. Fictive contraction recordings demonstrate endogenous motoneuron burst frequencies consistent with the neuromuscular system operating within the range of greatest plasticity. Genetic and pharmacological manipulations of critical components of pre- and postsynaptic Ca2+ regulation significantly affect the strength and time course of muscle contractions. A screen for modulators of the excitation-contraction machinery identified a FMRFa peptide, TPAEDFMRFa and its associated signalling pathway, that dramatically increases muscle performance. Drosophila serves as an excellent model for dissecting components of the excitation-contraction coupling machinery.
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Affiliation(s)
- Kiel G Ormerod
- The Picower Institute for Learning and Memory, Department of Biology, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - J Troy Littleton
- The Picower Institute for Learning and Memory, Department of Biology, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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15
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Yin C, Peterman E, Rasmussen JP, Parrish JZ. Transparent Touch: Insights From Model Systems on Epidermal Control of Somatosensory Innervation. Front Cell Neurosci 2021; 15:680345. [PMID: 34135734 PMCID: PMC8200473 DOI: 10.3389/fncel.2021.680345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 04/28/2021] [Indexed: 12/28/2022] Open
Abstract
Somatosensory neurons (SSNs) densely innervate our largest organ, the skin, and shape our experience of the world, mediating responses to sensory stimuli including touch, pressure, and temperature. Historically, epidermal contributions to somatosensation, including roles in shaping innervation patterns and responses to sensory stimuli, have been understudied. However, recent work demonstrates that epidermal signals dictate patterns of SSN skin innervation through a variety of mechanisms including targeting afferents to the epidermis, providing instructive cues for branching morphogenesis, growth control and structural stability of neurites, and facilitating neurite-neurite interactions. Here, we focus onstudies conducted in worms (Caenorhabditis elegans), fruit flies (Drosophila melanogaster), and zebrafish (Danio rerio): prominent model systems in which anatomical and genetic analyses have defined fundamental principles by which epidermal cells govern SSN development.
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Affiliation(s)
| | | | | | - Jay Z. Parrish
- Department of Biology, University of Washington, Seattle, WA, United States
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16
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Mase A, Augsburger J, Brückner K. Macrophages and Their Organ Locations Shape Each Other in Development and Homeostasis - A Drosophila Perspective. Front Cell Dev Biol 2021; 9:630272. [PMID: 33777939 PMCID: PMC7991785 DOI: 10.3389/fcell.2021.630272] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
Across the animal kingdom, macrophages are known for their functions in innate immunity, but they also play key roles in development and homeostasis. Recent insights from single cell profiling and other approaches in the invertebrate model organism Drosophila melanogaster reveal substantial diversity among Drosophila macrophages (plasmatocytes). Together with vertebrate studies that show genuine expression signatures of macrophages based on their organ microenvironments, it is expected that Drosophila macrophage functional diversity is shaped by their anatomical locations and systemic conditions. In vivo evidence for diverse macrophage functions has already been well established by Drosophila genetics: Drosophila macrophages play key roles in various aspects of development and organogenesis, including embryogenesis and development of the nervous, digestive, and reproductive systems. Macrophages further maintain homeostasis in various organ systems and promote regeneration following organ damage and injury. The interdependence and interplay of tissues and their local macrophage populations in Drosophila have implications for understanding principles of organ development and homeostasis in a wide range of species.
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Affiliation(s)
- Anjeli Mase
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, United States
| | - Jordan Augsburger
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, United States
| | - Katja Brückner
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, United States
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, United States
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17
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Morpho-Functional Consequences of Swiss Cheese Knockdown in Glia of Drosophila melanogaster. Cells 2021; 10:cells10030529. [PMID: 33801404 PMCID: PMC7998100 DOI: 10.3390/cells10030529] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 01/15/2023] Open
Abstract
Glia are crucial for the normal development and functioning of the nervous system in many animals. Insects are widely used for studies of glia genetics and physiology. Drosophila melanogaster surface glia (perineurial and subperineurial) form a blood–brain barrier in the central nervous system and blood–nerve barrier in the peripheral nervous system. Under the subperineurial glia layer, in the cortical region of the central nervous system, cortex glia encapsulate neuronal cell bodies, whilst in the peripheral nervous system, wrapping glia ensheath axons of peripheral nerves. Here, we show that the expression of the evolutionarily conserved swiss cheese gene is important in several types of glia. swiss cheese knockdown in subperineurial glia leads to morphological abnormalities of these cells. We found that the number of subperineurial glia nuclei is reduced under swiss cheese knockdown, possibly due to apoptosis. In addition, the downregulation of swiss cheese in wrapping glia causes a loss of its integrity. We reveal transcriptome changes under swiss cheese knockdown in subperineurial glia and in cortex + wrapping glia and show that the downregulation of swiss cheese in these types of glia provokes reactive oxygen species acceleration. These results are accompanied by a decline in animal mobility measured by the negative geotaxis performance assay.
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18
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Rossi AM, Jafari S, Desplan C. Integrated Patterning Programs During Drosophila Development Generate the Diversity of Neurons and Control Their Mature Properties. Annu Rev Neurosci 2021; 44:153-172. [PMID: 33556251 DOI: 10.1146/annurev-neuro-102120-014813] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
During the approximately 5 days of Drosophila neurogenesis (late embryogenesis to the beginning of pupation), a limited number of neural stem cells produce approximately 200,000 neurons comprising hundreds of cell types. To build a functional nervous system, neuronal types need to be produced in the proper places, appropriate numbers, and correct times. We discuss how neural stem cells (neuroblasts) obtain so-called area codes for their positions in the nervous system (spatial patterning) and how they keep time to sequentially produce neurons with unique fates (temporal patterning). We focus on specific examples that demonstrate how a relatively simple patterning system (Notch) can be used reiteratively to generate different neuronal types. We also speculate on how different modes of temporal patterning that operate over short versus long time periods might be linked. We end by discussing how specification programs are integrated and lead to the terminal features of different neuronal types.
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Affiliation(s)
- Anthony M Rossi
- Department of Biology, New York University, New York, NY 10003, USA; .,Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shadi Jafari
- Department of Biology, New York University, New York, NY 10003, USA;
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA;
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19
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Gallicchio L, Griffiths-Jones S, Ronshaugen M. Single-cell visualization of mir-9a and Senseless co-expression during Drosophila melanogaster embryonic and larval peripheral nervous system development. G3-GENES GENOMES GENETICS 2021; 11:6044132. [PMID: 33561238 PMCID: PMC7849905 DOI: 10.1093/g3journal/jkaa010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/16/2020] [Indexed: 11/17/2022]
Abstract
The Drosophila melanogaster peripheral nervous system (PNS) comprises the sensory organs that allow the fly to detect environmental factors such as temperature and pressure. PNS development is a highly specified process where each sensilla originates from a single sensory organ precursor (SOP) cell. One of the major genetic orchestrators of PNS development is Senseless, which encodes a zinc finger transcription factor (Sens). Sens is both necessary and sufficient for SOP differentiation. Senseless expression and SOP number are regulated by the microRNA miR-9a. However, the reciprocal dynamics of Senseless and miR-9a are still obscure. By coupling single-molecule FISH with immunofluorescence, we are able to visualize transcription of the mir-9a locus and expression of Sens simultaneously. During embryogenesis, we show that the expression of mir-9a in SOP cells is rapidly lost as Senseless expression increases. However, this mutually exclusive expression pattern is not observed in the third instar imaginal wing disc, where some Senseless-expressing cells show active sites of mir-9a transcription. These data challenge and extend previous models of Senseless regulation and show complex co-expression dynamics between mir-9a and Senseless. The differences in this dynamic relationship between embryonic and larval PNS development suggest a possible switch in miR-9a function. Our work brings single-cell resolution to the understanding of dynamic regulation of PNS development by Senseless and miR-9a.
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Affiliation(s)
- Lorenzo Gallicchio
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Matthew Ronshaugen
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
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20
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Hartwig C, Méndez GM, Bhattacharjee S, Vrailas-Mortimer AD, Zlatic SA, Freeman AAH, Gokhale A, Concilli M, Werner E, Sapp Savas C, Rudin-Rush S, Palmer L, Shearing N, Margewich L, McArthy J, Taylor S, Roberts B, Lupashin V, Polishchuk RS, Cox DN, Jorquera RA, Faundez V. Golgi-Dependent Copper Homeostasis Sustains Synaptic Development and Mitochondrial Content. J Neurosci 2021; 41:215-233. [PMID: 33208468 PMCID: PMC7810662 DOI: 10.1523/jneurosci.1284-20.2020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/02/2020] [Accepted: 11/09/2020] [Indexed: 01/05/2023] Open
Abstract
Rare genetic diseases preponderantly affect the nervous system causing neurodegeneration to neurodevelopmental disorders. This is the case for both Menkes and Wilson disease, arising from mutations in ATP7A and ATP7B, respectively. The ATP7A and ATP7B proteins localize to the Golgi and regulate copper homeostasis. We demonstrate genetic and biochemical interactions between ATP7 paralogs with the conserved oligomeric Golgi (COG) complex, a Golgi apparatus vesicular tether. Disruption of Drosophila copper homeostasis by ATP7 tissue-specific transgenic expression caused alterations in epidermis, aminergic, sensory, and motor neurons. Prominent among neuronal phenotypes was a decreased mitochondrial content at synapses, a phenotype that paralleled with alterations of synaptic morphology, transmission, and plasticity. These neuronal and synaptic phenotypes caused by transgenic expression of ATP7 were rescued by downregulation of COG complex subunits. We conclude that the integrity of Golgi-dependent copper homeostasis mechanisms, requiring ATP7 and COG, are necessary to maintain mitochondria functional integrity and localization to synapses.SIGNIFICANCE STATEMENT Menkes and Wilson disease affect copper homeostasis and characteristically afflict the nervous system. However, their molecular neuropathology mechanisms remain mostly unexplored. We demonstrate that copper homeostasis in neurons is maintained by two factors that localize to the Golgi apparatus, ATP7 and the conserved oligomeric Golgi (COG) complex. Disruption of these mechanisms affect mitochondrial function and localization to synapses as well as neurotransmission and synaptic plasticity. These findings suggest communication between the Golgi apparatus and mitochondria through homeostatically controlled cellular copper levels and copper-dependent enzymatic activities in both organelles.
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Affiliation(s)
- Cortnie Hartwig
- Departments of Cell Biology, Emory University, Atlanta, Georgia 30322
| | | | - Shatabdi Bhattacharjee
- Neuroscience Institute, Center for Behavioral Neuroscience, Georgia State University, Atlanta, Georgia 30302
| | | | | | - Amanda A H Freeman
- The Center for the Study of Human Health, Emory University, Atlanta, Georgia 30322
| | - Avanti Gokhale
- Departments of Cell Biology, Emory University, Atlanta, Georgia 30322
| | - Mafalda Concilli
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli 80078, Italy
| | - Erica Werner
- Departments of Cell Biology, Emory University, Atlanta, Georgia 30322
| | | | | | - Laura Palmer
- Departments of Cell Biology, Emory University, Atlanta, Georgia 30322
| | - Nicole Shearing
- Departments of Cell Biology, Emory University, Atlanta, Georgia 30322
| | - Lindsey Margewich
- School of Biological Sciences, IL State University, Normal, Illinois 617901
| | - Jacob McArthy
- School of Biological Sciences, IL State University, Normal, Illinois 617901
| | - Savanah Taylor
- School of Biological Sciences, IL State University, Normal, Illinois 617901
| | - Blaine Roberts
- Departments of Biochemistry, Emory University, Atlanta, Georgia 30322
| | - Vladimir Lupashin
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Roman S Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli 80078, Italy
| | - Daniel N Cox
- Neuroscience Institute, Center for Behavioral Neuroscience, Georgia State University, Atlanta, Georgia 30302
| | - Ramon A Jorquera
- Neuroscience Department, Universidad Central del Caribe, Bayamon, Puerto Rico 00956
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile
| | - Victor Faundez
- Departments of Cell Biology, Emory University, Atlanta, Georgia 30322
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21
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Aboukilila MY, Sami JD, Wang J, England W, Spitale RC, Cleary MD. Identification of novel regulators of dendrite arborization using cell type-specific RNA metabolic labeling. PLoS One 2020; 15:e0240386. [PMID: 33264304 PMCID: PMC7710095 DOI: 10.1371/journal.pone.0240386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/06/2020] [Indexed: 11/18/2022] Open
Abstract
Obtaining neuron transcriptomes is challenging; their complex morphology and interconnected microenvironments make it difficult to isolate neurons without potentially altering gene expression. Multidendritic sensory neurons (md neurons) of Drosophila larvae are commonly used to study peripheral nervous system biology, particularly dendrite arborization. We sought to test if EC-tagging, a biosynthetic RNA tagging and purification method that avoids the caveats of physical isolation, would enable discovery of novel regulators of md neuron dendrite arborization. Our aims were twofold: discover novel md neuron transcripts and test the sensitivity of EC-tagging. RNAs were biosynthetically tagged by expressing CD:UPRT (a nucleobase-converting fusion enzyme) in md neurons and feeding 5-ethynylcytosine (EC) to larvae. Only CD:UPRT-expressing cells are competent to convert EC into 5-ethynyluridine-monophosphate which is subsequently incorporated into nascent RNA transcripts. Tagged RNAs were purified and used for RNA-sequencing. Reference RNA was prepared in a similar manner using 5-ethynyluridine (EUd) to tag RNA in all cells and negative control RNA-seq was performed on "mock tagged" samples to identify non-specifically purified transcripts. Differential expression analysis identified md neuron enriched and depleted transcripts. Three candidate genes encoding RNA-binding proteins (RBPs) were tested for a role in md neuron dendrite arborization. Loss-of-function for the m6A-binding factor Ythdc1 did not cause any dendrite arborization defects while RNAi of the other two candidates, the poly(A) polymerase Hiiragi and the translation regulator Hephaestus, caused significant defects in dendrite arborization. This work provides an expanded view of transcription in md neurons and a technical framework for combining EC-tagging with RNA-seq to profile transcription in cells that may not be amenable to physical isolation.
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Affiliation(s)
- Mohamed Y. Aboukilila
- Department of Molecular and Cell Biology, Quantitative and Systems Biology Graduate Program, University of California, Merced, CA, United States of America
| | - Josephine D. Sami
- Department of Molecular and Cell Biology, Quantitative and Systems Biology Graduate Program, University of California, Merced, CA, United States of America
| | - Jingtian Wang
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, CA, United States of America
| | - Whitney England
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, CA, United States of America
| | - Robert C. Spitale
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, CA, United States of America
| | - Michael D. Cleary
- Department of Molecular and Cell Biology, Quantitative and Systems Biology Graduate Program, University of California, Merced, CA, United States of America
- * E-mail:
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22
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Palavalli A, Tizón-Escamilla N, Rupprecht JF, Lecuit T. Deterministic and Stochastic Rules of Branching Govern Dendrite Morphogenesis of Sensory Neurons. Curr Biol 2020; 31:459-472.e4. [PMID: 33212017 DOI: 10.1016/j.cub.2020.10.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/22/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023]
Abstract
Dendrite morphology is necessary for the correct integration of inputs that neurons receive. The branching mechanisms allowing neurons to acquire their type-specific morphology remain unclear. Classically, axon and dendrite patterns were shown to be guided by molecules, providing deterministic cues. However, the extent to which deterministic and stochastic mechanisms, based upon purely statistical bias, contribute to the emergence of dendrite shape is largely unknown. We address this issue using the Drosophila class I vpda multi-dendritic neurons. Detailed quantitative analysis of vpda dendrite morphogenesis indicates that the primary branch grows very robustly in a fixed direction, though secondary branch numbers and lengths showed fluctuations characteristic of stochastic systems. Live-tracking dendrites and computational modeling revealed how neuron shape emerges from few local statistical parameters of branch dynamics. We report key opposing aspects of how tree architecture feedbacks on the local probability of branch shrinkage. Child branches promote stabilization of parent branches, although self-repulsion promotes shrinkage. Finally, we show that self-repulsion, mediated by the adhesion molecule Dscam1, indirectly patterns the growth of secondary branches by spatially restricting their direction of stable growth perpendicular to the primary branch. Thus, the stochastic nature of secondary branch dynamics and the existence of geometric feedback emphasize the importance of self-organization in neuronal dendrite morphogenesis.
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Affiliation(s)
- Amrutha Palavalli
- Aix Marseille Université and CNRS, IBDM - UMR7288 and Turing Centre for Living Systems Campus de Luminy Case 907, Marseille 13288, France
| | - Nicolás Tizón-Escamilla
- Aix-Marseille Université, Université de Toulon, CNRS, CPT, Turing Centre for Living Systems Campus de Luminy Case 907, Marseille 13288, France
| | - Jean-François Rupprecht
- Aix-Marseille Université, Université de Toulon, CNRS, CPT, Turing Centre for Living Systems Campus de Luminy Case 907, Marseille 13288, France.
| | - Thomas Lecuit
- Aix Marseille Université and CNRS, IBDM - UMR7288 and Turing Centre for Living Systems Campus de Luminy Case 907, Marseille 13288, France; Collège de France, 11 Place Marcelin Berthelot, Paris 75005, France.
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23
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Molecular Basis for Cephalic Mechanosensitivity of Drosophila Larvae. Neurosci Bull 2020; 36:1051-1056. [PMID: 32761438 DOI: 10.1007/s12264-020-00555-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/03/2020] [Indexed: 10/23/2022] Open
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24
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Bittern J, Pogodalla N, Ohm H, Brüser L, Kottmeier R, Schirmeier S, Klämbt C. Neuron-glia interaction in the Drosophila nervous system. Dev Neurobiol 2020; 81:438-452. [PMID: 32096904 DOI: 10.1002/dneu.22737] [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: 11/11/2019] [Revised: 02/11/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022]
Abstract
Animals are able to move and react in manifold ways to external stimuli. Thus, environmental stimuli need to be detected, information must be processed, and, finally, an output decision must be transmitted to the musculature to get the animal moving. All these processes depend on the nervous system which comprises an intricate neuronal network and many glial cells. Glial cells have an equally important contribution in nervous system function as their neuronal counterpart. Manifold roles are attributed to glia ranging from controlling neuronal cell number and axonal pathfinding to regulation of synapse formation, function, and plasticity. Glial cells metabolically support neurons and contribute to the blood-brain barrier. All of the aforementioned aspects require extensive cell-cell interactions between neurons and glial cells. Not surprisingly, many of these processes are found in all phyla executed by evolutionarily conserved molecules. Here, we review the recent advance in understanding neuron-glia interaction in Drosophila melanogaster to suggest that work in simple model organisms will shed light on the function of mammalian glial cells, too.
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Affiliation(s)
- Jonas Bittern
- Institut für Neuro- und Verhaltensbiologie, Universität Münster, Münster, Germany
| | - Nicole Pogodalla
- Institut für Neuro- und Verhaltensbiologie, Universität Münster, Münster, Germany
| | - Henrike Ohm
- Institut für Neuro- und Verhaltensbiologie, Universität Münster, Münster, Germany
| | - Lena Brüser
- Institut für Neuro- und Verhaltensbiologie, Universität Münster, Münster, Germany
| | - Rita Kottmeier
- Institut für Neuro- und Verhaltensbiologie, Universität Münster, Münster, Germany
| | - Stefanie Schirmeier
- Institut für Neuro- und Verhaltensbiologie, Universität Münster, Münster, Germany
| | - Christian Klämbt
- Institut für Neuro- und Verhaltensbiologie, Universität Münster, Münster, Germany
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25
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Crews ST. Drosophila Embryonic CNS Development: Neurogenesis, Gliogenesis, Cell Fate, and Differentiation. Genetics 2019; 213:1111-1144. [PMID: 31796551 PMCID: PMC6893389 DOI: 10.1534/genetics.119.300974] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/26/2019] [Indexed: 01/04/2023] Open
Abstract
The Drosophila embryonic central nervous system (CNS) is a complex organ consisting of ∼15,000 neurons and glia that is generated in ∼1 day of development. For the past 40 years, Drosophila developmental neuroscientists have described each step of CNS development in precise molecular genetic detail. This has led to an understanding of how an intricate nervous system emerges from a single cell. These studies have also provided important, new concepts in developmental biology, and provided an essential model for understanding similar processes in other organisms. In this article, the key genes that guide Drosophila CNS development and how they function is reviewed. Features of CNS development covered in this review are neurogenesis, gliogenesis, cell fate specification, and differentiation.
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Affiliation(s)
- Stephen T Crews
- Department of Biochemistry and Biophysics, Integrative Program for Biological and Genome Sciences, School of Medicine, The University of North Carolina at Chapel Hill, North Carolina 27599
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26
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Lopez-Bellido R, Himmel NJ, Gutstein HB, Cox DN, Galko MJ. An assay for chemical nociception in Drosophila larvae. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190282. [PMID: 31544619 PMCID: PMC6790381 DOI: 10.1098/rstb.2019.0282] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2019] [Indexed: 12/14/2022] Open
Abstract
Chemically induced nociception has not yet been studied intensively in genetically tractable models. Hence, our goal was to establish a Drosophila assay that can be used to study the cellular and molecular/genetic bases of chemically induced nociception. Drosophila larvae exposed to increasing concentrations of hydrochloric acid (HCl) produced an increasingly intense aversive rolling response. HCl (0.5%) was subthreshold and provoked no response. All classes of peripheral multidendritic (md) sensory neurons (classes I-IV) are required for full responsiveness to acid, with class IV making the largest contribution. At the cellular level, classes IV, III and I showed increases in calcium following acid exposure. In the central nervous system, Basin-4 second-order neurons are the key regulators of chemically induced nociception, with a slight contribution from other types. Finally, chemical nociception can be sensitized by tissue damage. Subthreshold HCl provoked chemical allodynia in larvae 4 h after physical puncture wounding. Pinch wounding and UV irradiation, which do not compromise the cuticle, did not cause chemical allodynia. In sum, we developed a novel assay to study chemically induced nociception in Drosophila larvae. This assay, combined with the high genetic resolving power of Drosophila, should improve our basic understanding of fundamental mechanisms of chemical nociception. This article is part of the Theo Murphy meeting issue 'Evolution of mechanisms and behaviour important for pain'.
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Affiliation(s)
- Roger Lopez-Bellido
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Anesthesiology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Nathaniel J. Himmel
- Neuroscience Institute, Georgia State University, P.O. Box 5030, Atlanta, GA 30303, USA
| | - Howard B. Gutstein
- Department of Anesthesiology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Daniel N. Cox
- Neuroscience Institute, Georgia State University, P.O. Box 5030, Atlanta, GA 30303, USA
| | - Michael J. Galko
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Neuroscience Graduate Program, The MD Anderson UT Health Graduate School of Biomedical Sciences, TX 77030, USA
- Genetics and Epigenetics Graduate Program, The MD Anderson UT Health Graduate School of Biomedical Sciences, TX 77030, USA
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27
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Analyzing chemotherapy-induced peripheral neuropathy in vivo using non-mammalian animal models. Exp Neurol 2019; 323:113090. [PMID: 31669484 DOI: 10.1016/j.expneurol.2019.113090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/19/2019] [Accepted: 10/23/2019] [Indexed: 12/31/2022]
Abstract
Non-mammalian models of CIPN remain relatively sparse, but the knowledge gained from the few published studies suggest that these species have great potential to serve as a discovery platform for new pathways and underlying genetic mechanisms of CIPN. These models permit large-scale genetic and pharmacological screening, and they are highly suitable for in vivo imaging. CIPN phenotypes described in rodents have been confirmed in those models, and conversely, genetic players leading to axon de- and regeneration under conditions of chemotherapy treatment identified in these non-mammalian species have been validated in rodents. Given the need for non-traditional approaches with which to identify new CIPN mechanisms, these models bear a strong potential due to the conservation of basic mechanisms by which chemotherapeutic agents induce neurotoxicity.
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28
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Gonsior M, Ismat A. sli is required for proper morphology and migration of sensory neurons in the Drosophila PNS. Neural Dev 2019; 14:10. [PMID: 31651354 PMCID: PMC6813078 DOI: 10.1186/s13064-019-0135-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/17/2019] [Indexed: 11/12/2022] Open
Abstract
Neurons and glial cells coordinate with each other in many different aspects of nervous system development. Both types of cells are receiving multiple guidance cues to guide the neurons and glial cells to their proper final position. The lateral chordotonal organs (lch5) of the Drosophila peripheral nervous system (PNS) are composed of five sensory neurons surrounded by four different glial cells, scolopale cells, cap cells, attachment cells and ligament cells. During embryogenesis, the lch5 neurons go through a rotation and ventral migration to reach their final position in the lateral region of the abdomen. We show here that the extracellular ligand sli is required for the proper ventral migration and morphology of the lch5 neurons. We further show that mutations in the Sli receptors Robo and Robo2 also display similar defects as loss of sli, suggesting a role for Slit-Robo signaling in lch5 migration and positioning. Additionally, we demonstrate that the scolopale, cap and attachment cells follow the mis-migrated lch5 neurons in sli mutants, while the ventral stretching of the ligament cells seems to be independent of the lch5 neurons. This study sheds light on the role of Slit-Robo signaling in sensory neuron development.
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Affiliation(s)
- Madison Gonsior
- Department of Biology, University of St. Thomas, Saint Paul, MN, 55104, USA
| | - Afshan Ismat
- Department of Biology, University of St. Thomas, Saint Paul, MN, 55104, USA.
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29
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Wilson C, Kavaler J, Ahmad ST. Expression of a human variant of CHMP2B linked to neurodegeneration in Drosophila external sensory organs leads to cell fate transformations associated with increased Notch activity. Dev Neurobiol 2019; 80:85-97. [PMID: 31587468 DOI: 10.1002/dneu.22722] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/19/2019] [Accepted: 10/02/2019] [Indexed: 02/06/2023]
Abstract
Proper function of cell signaling pathways is dependent upon regulated membrane trafficking events that lead to the endocytosis, recycling, and degradation of cell surface receptors. The endosomal complexes required for transport (ESCRT) genes play a critical role in the sorting of ubiquitinated cell surface proteins. CHMP2BIntron5 , a truncated form of a human ESCRT-III protein, was discovered in a Danish family afflicted by a hereditary form of frontotemporal dementia (FTD). Although the mechanism by which the CHMP2B mutation in this family causes FTD is unknown, the resulting protein has been shown to disrupt normal endosomal-lysosomal pathway function and leads to aberrant regulation of signaling pathways. Here we have misexpressed CHMP2BIntron5 in the developing Drosophila external sensory (ES) organ lineage and demonstrate that it is capable of altering cell fates. Each of the cell fate transformations seen is compatible with an increase in Notch signaling. Furthermore, this interpretation is supported by evidence that expression of CHMP2BIntron5 in the notum environment is capable of raising the levels of Notch signaling. As such, these results add to a growing body of evidence that CHMP2BIntron5 can act rapidly to disrupt normal cellular function via the misregulation of critical cell surface receptor function.
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30
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Nisha, Aggarwal P, Sarkar S. Adequate expression of Globin1 is required for development and maintenance of nervous system in Drosophila. Mol Cell Neurosci 2019; 100:103398. [DOI: 10.1016/j.mcn.2019.103398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/07/2019] [Accepted: 08/25/2019] [Indexed: 10/26/2022] Open
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31
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Growth Factor Signaling Regulates Mechanical Nociception in Flies and Vertebrates. J Neurosci 2019; 39:6012-6030. [PMID: 31138657 DOI: 10.1523/jneurosci.2950-18.2019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 02/06/2023] Open
Abstract
Mechanical sensitization is one of the most difficult clinical pain problems to treat. However, the molecular and genetic bases of mechanical nociception are unclear. Here we develop a Drosophila model of mechanical nociception to investigate the ion channels and signaling pathways that regulate mechanical nociception. We fabricated von Frey filaments that span the subthreshold to high noxious range for Drosophila larvae. Using these, we discovered that pressure (force/area), rather than force per se, is the main determinant of aversive rolling responses to noxious mechanical stimuli. We demonstrated that the RTK PDGF/VEGF receptor (Pvr) and its ligands (Pvfs 2 and 3) are required for mechanical nociception and normal dendritic branching. Pvr is expressed and functions in class IV sensory neurons, whereas Pvf2 and Pvf3 are produced by multiple tissues. Constitutive overexpression of Pvr and its ligands or inducible overexpression of Pvr led to mechanical hypersensitivity that could be partially separated from morphological effects. Genetic analyses revealed that the Piezo and Pain ion channels are required for mechanical hypersensitivity observed upon ectopic activation of Pvr signaling. PDGF, but not VEGF, peptides caused mechanical hypersensitivity in rats. Pharmacological inhibition of VEGF receptor Type 2 (VEGFR-2) signaling attenuated mechanical nociception in rats, suggesting a conserved role for PDGF and VEGFR-2 signaling in regulating mechanical nociception. VEGFR-2 inhibition also attenuated morphine analgesic tolerance in rats. Our results reveal that a conserved RTK signaling pathway regulates baseline mechanical nociception in flies and rats.SIGNIFICANCE STATEMENT Hypersensitivity to touch is poorly understood and extremely difficult to treat. Using a refined Drosophila model of mechanical nociception, we discovered a conserved VEGF-related receptor tyrosine kinase signaling pathway that regulates mechanical nociception in flies. Importantly, pharmacological inhibition of VEGF receptor Type 2 signaling in rats causes analgesia and blocks opioid tolerance. We have thus established a robust, genetically tractable system for the rapid identification and functional analysis of conserved genes underlying mechanical pain sensitivity.
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32
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Kuehn ED, Meltzer S, Abraira VE, Ho CY, Ginty DD. Tiling and somatotopic alignment of mammalian low-threshold mechanoreceptors. Proc Natl Acad Sci U S A 2019; 116:9168-9177. [PMID: 30996124 PMCID: PMC6511030 DOI: 10.1073/pnas.1901378116] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Innocuous mechanical stimuli acting on the skin are detected by sensory neurons, known as low-threshold mechanoreceptors (LTMRs). LTMRs are classified based on their response properties, action potential conduction velocity, rate of adaptation to static indentation of the skin, and terminal anatomy. Here, we report organizational properties of the cutaneous and central axonal projections of the five principal hairy skin LTMR subtypes. We find that axons of neurons within a particular LTMR class are largely nonoverlapping with respect to their cutaneous end organs (e.g., hair follicles), with Aβ rapidly adapting-LTMRs being the sole exception. Individual neurons of each LTMR class are mostly nonoverlapping with respect to their associated hair follicles, with the notable exception of C-LTMRs, which exhibit multiple branches that redundantly innervate individual hair follicles. In the spinal cord, LTMR central projections exhibit rostrocaudal elongation and mediolateral compression, compared with their cutaneous innervation patterns, and these central projections also exhibit a fine degree of homotypic topographic adjacency. These findings thus reveal homotypic tiling of LTMR subtype axonal projections in hairy skin and a remarkable degree of spatial precision of spinal cord axonal termination patterns, suggesting a somatotopically precise tactile encoding capability of the mechanosensory dorsal horn.
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Affiliation(s)
- Emily D Kuehn
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Shan Meltzer
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
| | - Victoria E Abraira
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
| | - Cheng-Ying Ho
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - David D Ginty
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115;
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
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33
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Stürner T, Tatarnikova A, Mueller J, Schaffran B, Cuntz H, Zhang Y, Nemethova M, Bogdan S, Small V, Tavosanis G. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development 2019; 146:dev.171397. [PMID: 30910826 DOI: 10.1242/dev.171397] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/08/2019] [Indexed: 01/02/2023]
Abstract
The formation of neuronal dendrite branches is fundamental for the wiring and function of the nervous system. Indeed, dendrite branching enhances the coverage of the neuron's receptive field and modulates the initial processing of incoming stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process of de novo branch formation, branch extension and retraction. The first step towards branch formation is the generation of a dynamic filopodium-like branchlet. The mechanisms underlying the initiation of dendrite branchlets are therefore crucial to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular localization of actin during the process of branching of Drosophila larva sensory neurons, combined with genetic analysis and electron tomography, we have identified the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved in the initiation of dendrite branchlet formation, under the control of the activator WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component marks the site of branchlet initiation in vivo These data position the activation of Arp2/3 as an early hub for the initiation of branchlet formation.
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Affiliation(s)
- Tomke Stürner
- Deutsches Zentrum für Neurodegenerative Erkrankungen e.V./German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Anastasia Tatarnikova
- Deutsches Zentrum für Neurodegenerative Erkrankungen e.V./German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany.,MPI for Neurobiology, 82152 Munich- Martinsried, Germany
| | - Jan Mueller
- Institute of Molecular biotechnology (IMBA), 1030 Wien, Austria
| | - Barbara Schaffran
- Deutsches Zentrum für Neurodegenerative Erkrankungen e.V./German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Hermann Cuntz
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, 60528 Frankfurt, Germany.,Frankfurt Institute for Advanced Studies, 60438 Frankfurt, Germany
| | - Yun Zhang
- Deutsches Zentrum für Neurodegenerative Erkrankungen e.V./German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Maria Nemethova
- Institute of Molecular biotechnology (IMBA), 1030 Wien, Austria
| | - Sven Bogdan
- Institut für Physiologie und Pathophysiologie, Abteilung Molekulare Zellphysiologie, Phillips-Universität Marburg, 35037 Marburg, Germany
| | - Vic Small
- Institute of Molecular biotechnology (IMBA), 1030 Wien, Austria
| | - Gaia Tavosanis
- Deutsches Zentrum für Neurodegenerative Erkrankungen e.V./German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
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34
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Clark MQ, Zarin AA, Carreira-Rosario A, Doe CQ. Neural circuits driving larval locomotion in Drosophila. Neural Dev 2018; 13:6. [PMID: 29673388 PMCID: PMC5907184 DOI: 10.1186/s13064-018-0103-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/05/2018] [Indexed: 11/10/2022] Open
Abstract
More than 30 years of studies into Drosophila melanogaster neurogenesis have revealed fundamental insights into our understanding of axon guidance mechanisms, neural differentiation, and early cell fate decisions. What is less understood is how a group of neurons from disparate anterior-posterior axial positions, lineages and developmental periods of neurogenesis coalesce to form a functional circuit. Using neurogenetic techniques developed in Drosophila it is now possible to study the neural substrates of behavior at single cell resolution. New mapping tools described in this review, allow researchers to chart neural connectivity to better understand how an anatomically simple organism performs complex behaviors.
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Affiliation(s)
- Matthew Q Clark
- Institute of Neuroscience, Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, OR, 97403, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasedena, CA, 91125, USA
| | - Aref Arzan Zarin
- Institute of Neuroscience, Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, OR, 97403, USA
| | | | - Chris Q Doe
- Institute of Neuroscience, Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, OR, 97403, USA.
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35
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Morphological determinants of dendritic arborization neurons in Drosophila larva. Brain Struct Funct 2017; 223:1107-1120. [PMID: 29094302 DOI: 10.1007/s00429-017-1541-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 10/19/2017] [Indexed: 01/08/2023]
Abstract
Pairing in vivo imaging and computational modeling of dendritic arborization (da) neurons from the fruit fly larva provides a unique window into neuronal growth and underlying molecular processes. We image, reconstruct, and analyze the morphology of wild-type, RNAi-silenced, and mutant da neurons. We then use local and global rule-based stochastic simulations to generate artificial arbors, and identify the parameters that statistically best approximate the real data. We observe structural homeostasis in all da classes, where an increase in size of one dendritic stem is compensated by a reduction in the other stems of the same neuron. Local rule models show that bifurcation probability is determined by branch order, while branch length depends on path distance from the soma. Global rule simulations suggest that most complex morphologies tend to be constrained by resource optimization, while simpler neuron classes privilege path distance conservation. Genetic manipulations affect both the local and global optimal parameters, demonstrating functional perturbations in growth mechanisms.
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36
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Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster. PLoS Comput Biol 2017; 13:e1005791. [PMID: 29045400 PMCID: PMC5662236 DOI: 10.1371/journal.pcbi.1005791] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 10/30/2017] [Accepted: 09/25/2017] [Indexed: 11/19/2022] Open
Abstract
Accurate gene or protein function prediction is a key challenge in the post-genome era. Most current methods perform well on molecular function prediction, but struggle to provide useful annotations relating to biological process functions due to the limited power of sequence-based features in that functional domain. In this work, we systematically evaluate the predictive power of temporal transcription expression profiles for protein function prediction in Drosophila melanogaster. Our results show significantly better performance on predicting protein function when transcription expression profile-based features are integrated with sequence-derived features, compared with the sequence-derived features alone. We also observe that the combination of expression-based and sequence-based features leads to further improvement of accuracy on predicting all three domains of gene function. Based on the optimal feature combinations, we then propose a novel multi-classifier-based function prediction method for Drosophila melanogaster proteins, FFPred-fly+. Interpreting our machine learning models also allows us to identify some of the underlying links between biological processes and developmental stages of Drosophila melanogaster. Despite painstaking experimental efforts and the extensive sequence similarity based annotation transfers, less than a half of the fruit fly protein sequences in UniProtKB have some functional annotation. To help fill in this gap, we test the usefulness of publicly available temporal gene expression profiles and their combination with many biophysical attributes that can be effectively derived from the corresponding protein sequence. We find that such an integrative function prediction method provides more accurate predictions than using sequence data alone and we expect these predictions to help narrow down the number of experimental assays required to characterise fly protein function. We demonstrate by highlighting correlations between predicted biological process functions and known facts about fly developmental stages.
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37
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Abstract
Neurons allocated to sense organs respond rapidly to mechanical signals dictating behavioral responses at the organism level. The receptors that transduce these signals, and underlie these senses, are mechanically gated channels. Research on mechanosensation over the past decade, employing in many cases Drosophila as a model, has focused in typifying these receptors and in exploring the different ways, depending on context, in which these mechanosensors are modulated. In this review, we discuss first what we have learned from Drosophila on these mechanisms and we describe the different mechanosensory organs present in the Drosophila larvae and adult. Secondly, we focus on the progress obtained by studying the fly on the characterization of the mechanosensory crosstalk underlying complex behaviors like motor coordination. Finally, turning to a cellular level, we summarize what is known on the mechanical properties and sensing capabilities of neural cells and how they may affect neural physiology and pathology.
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Affiliation(s)
- Katerina Karkali
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Parc Cientific de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Enrique Martin-Blanco
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Parc Cientific de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain.
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38
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Jo J, Im SH, Babcock DT, Iyer SC, Gunawan F, Cox DN, Galko MJ. Drosophila caspase activity is required independently of apoptosis to produce active TNF/Eiger during nociceptive sensitization. Cell Death Dis 2017; 8:e2786. [PMID: 28492538 PMCID: PMC5520682 DOI: 10.1038/cddis.2016.474] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 12/03/2016] [Accepted: 12/06/2016] [Indexed: 01/12/2023]
Abstract
Tumor necrosis factor (TNF) signaling is required for inflammatory nociceptive (pain) sensitization in Drosophila and vertebrates. Nociceptive sensitization in Drosophila larvae following UV-induced tissue damage is accompanied by epidermal apoptosis and requires epidermal-derived TNF/Eiger and the initiator caspase, Dronc. Major gaps remain regarding TNF function in sensitization, including the relationship between apoptosis/tissue damage and TNF production, the downstream signaling in this context, and the target genes that modulate nociceptive behaviors. Here, apoptotic cell death and thermal nociceptive sensitization are genetically and procedurally separable in a Drosophila model of UV-induced nociceptive sensitization. Activation of epidermal Dronc induces TNF-dependent but effector caspase-independent nociceptive sensitization in the absence of UV. In addition, knockdown of Dronc attenuated nociceptive sensitization induced by full-length TNF/Eiger but not by a constitutively soluble form. UV irradiation induced TNF production in both in vitro and in vivo, but TNF secretion into hemolymph was not sufficient to induce thermal nociceptive sensitization. Downstream mediators of TNF-induced sensitization included two TNF receptor-associated factors, a p38 kinase, and the transcription factor nuclear factor kappa B. Finally, sensory neuron-specific microarray analysis revealed downstream TNF target genes induced during thermal nociceptive sensitization. One of these, enhancer of zeste (E(z)), functions downstream of TNF during thermal nociceptive sensitization. Our findings suggest that an initiator caspase is involved in TNF processing/secretion during nociceptive sensitization, and that TNF activation leads to a specific downstream signaling cascade and gene transcription required for sensitization. These findings have implications for both the evolution of inflammatory caspase function following tissue damage signals and the action of TNF during sensitization in vertebrates.
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Affiliation(s)
- Juyeon Jo
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Genes and Development Graduate Program, Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Seol Hee Im
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel T Babcock
- Neuroscience Graduate Program, Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Srividya C Iyer
- Neuroscience Institute, Georgia State University, Atlanta, GA, USA
| | - Felona Gunawan
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX, USA
| | - Daniel N Cox
- Neuroscience Institute, Georgia State University, Atlanta, GA, USA
| | - Michael J Galko
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Genes and Development Graduate Program, Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Neuroscience Graduate Program, Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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39
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Salzberg Y, Coleman AJ, Celestrin K, Cohen-Berkman M, Biederer T, Henis-Korenblit S, Bülow HE. Reduced Insulin/Insulin-Like Growth Factor Receptor Signaling Mitigates Defective Dendrite Morphogenesis in Mutants of the ER Stress Sensor IRE-1. PLoS Genet 2017; 13:e1006579. [PMID: 28114319 PMCID: PMC5293268 DOI: 10.1371/journal.pgen.1006579] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/06/2017] [Accepted: 01/11/2017] [Indexed: 11/18/2022] Open
Abstract
Neurons receive excitatory or sensory inputs through their dendrites, which often branch extensively to form unique neuron-specific structures. How neurons regulate the formation of their particular arbor is only partially understood. In genetic screens using the multidendritic arbor of PVD somatosensory neurons in the nematode Caenorhabditis elegans, we identified a mutation in the ER stress sensor IRE-1/Ire1 (inositol requiring enzyme 1) as crucial for proper PVD dendrite arborization in vivo. We further found that regulation of dendrite growth in cultured rat hippocampal neurons depends on Ire1 function, showing an evolutionarily conserved role for IRE-1/Ire1 in dendrite patterning. PVD neurons of nematodes lacking ire-1 display reduced arbor complexity, whereas mutations in genes encoding other ER stress sensors displayed normal PVD dendrites, specifying IRE-1 as a selective ER stress sensor that is essential for PVD dendrite morphogenesis. Although structure function analyses indicated that IRE-1's nuclease activity is necessary for its role in dendrite morphogenesis, mutations in xbp-1, the best-known target of non-canonical splicing by IRE-1/Ire1, do not exhibit PVD phenotypes. We further determined that secretion and distal localization to dendrites of the DMA-1/leucine rich transmembrane receptor (DMA-1/LRR-TM) is defective in ire-1 but not xbp-1 mutants, suggesting a block in the secretory pathway. Interestingly, reducing Insulin/IGF1 signaling can bypass the secretory block and restore normal targeting of DMA-1, and consequently normal PVD arborization even in the complete absence of functional IRE-1. This bypass of ire-1 requires the DAF-16/FOXO transcription factor. In sum, our work identifies a conserved role for ire-1 in neuronal branching, which is independent of xbp-1, and suggests that arborization defects associated with neuronal pathologies may be overcome by reducing Insulin/IGF signaling and improving ER homeostasis and function.
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Affiliation(s)
- Yehuda Salzberg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Andrew J. Coleman
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States of America
| | - Kevin Celestrin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Moran Cohen-Berkman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Thomas Biederer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States of America
| | - Sivan Henis-Korenblit
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Hannes E. Bülow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
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40
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Kohsaka H, Guertin PA, Nose A. Neural Circuits Underlying Fly Larval Locomotion. Curr Pharm Des 2017; 23:1722-1733. [PMID: 27928962 PMCID: PMC5470056 DOI: 10.2174/1381612822666161208120835] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/01/2016] [Indexed: 12/17/2022]
Abstract
Locomotion is a complex motor behavior that may be expressed in different ways using a variety of strategies depending upon species and pathological or environmental conditions. Quadrupedal or bipedal walking, running, swimming, flying and gliding constitute some of the locomotor modes enabling the body, in all cases, to move from one place to another. Despite these apparent differences in modes of locomotion, both vertebrate and invertebrate species share, at least in part, comparable neural control mechanisms for locomotor rhythm and pattern generation and modulation. Significant advances have been made in recent years in studies of the genetic aspects of these control systems. Findings made specifically using Drosophila (fruit fly) models and preparations have contributed to further understanding of the key role of genes in locomotion. This review focuses on some of the main findings made in larval fruit flies while briefly summarizing the basic advantages of using this powerful animal model for studying the neural locomotor system.
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Affiliation(s)
- Hiroshi Kohsaka
- Department of Complexity Science and Engineering, University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Pierre A. Guertin
- Department of Psychiatry & Neurosciences, Laval University, Québec City, QC, Canada
| | - Akinao Nose
- Department of Complexity Science and Engineering, University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
- Department of Physics, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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41
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Abstract
The ability of animals to flexibly navigate through complex environments depends on the integration of sensory information with motor commands. The sensory modality most tightly linked to motor control is mechanosensation. Adaptive motor control depends critically on an animal's ability to respond to mechanical forces generated both within and outside the body. The compact neural circuits of insects provide appealing systems to investigate how mechanical cues guide locomotion in rugged environments. Here, we review our current understanding of mechanosensation in insects and its role in adaptive motor control. We first examine the detection and encoding of mechanical forces by primary mechanoreceptor neurons. We then discuss how central circuits integrate and transform mechanosensory information to guide locomotion. Because most studies in this field have been performed in locusts, cockroaches, crickets, and stick insects, the examples we cite here are drawn mainly from these 'big insects'. However, we also pay particular attention to the tiny fruit fly, Drosophila, where new tools are creating new opportunities, particularly for understanding central circuits. Our aim is to show how studies of big insects have yielded fundamental insights relevant to mechanosensation in all animals, and also to point out how the Drosophila toolkit can contribute to future progress in understanding mechanosensory processing.
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Affiliation(s)
- John C Tuthill
- Department of Physiology and Biophysics, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA.
| | - Rachel I Wilson
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA.
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42
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Johnson SA, Zitserman D, Roegiers F. Numb regulates the balance between Notch recycling and late-endosome targeting in Drosophila neural progenitor cells. Mol Biol Cell 2016; 27:2857-66. [PMID: 27466320 PMCID: PMC5025272 DOI: 10.1091/mbc.e15-11-0751] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 07/21/2016] [Indexed: 11/11/2022] Open
Abstract
Steady-state and pulse-labeling techniques are used to follow Notch receptors in sensory organ precursor cells in Drosophila. Numb and L(2)gl antagonize a pool of Notch receptors, and Numb promotes Notch targeting to late endosomes in Drosophila neural progenitors to regulate Notch signaling and cell fate. The Notch signaling pathway plays essential roles in both animal development and human disease. Regulation of Notch receptor levels in membrane compartments has been shown to affect signaling in a variety of contexts. Here we used steady-state and pulse-labeling techniques to follow Notch receptors in sensory organ precursor cells in Drosophila. We find that the endosomal adaptor protein Numb regulates levels of Notch receptor trafficking to Rab7-labeled late endosomes but not early endosomes. Using an assay we developed that labels different pools of Notch receptors as they move through the endocytic system, we show that Numb specifically suppresses a recycled Notch receptor subpopulation and that excess Notch signaling in numb mutants requires the recycling endosome GTPase Rab11 activity. Our data therefore suggest that Numb controls the balance between Notch receptor recycling and receptor targeting to late endosomes to regulate signaling output after asymmetric cell division in Drosophila neural progenitors.
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Affiliation(s)
- Seth A Johnson
- Fox Chase Cancer Center, Philadelphia, PA 19111 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Diana Zitserman
- Fox Chase Cancer Center, Philadelphia, PA 19111 University of Bridgeport, Bridgeport, CT 06604
| | - Fabrice Roegiers
- Fox Chase Cancer Center, Philadelphia, PA 19111 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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43
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Trimming of sequence reads alters RNA-Seq gene expression estimates. BMC Bioinformatics 2016; 17:103. [PMID: 26911985 PMCID: PMC4766705 DOI: 10.1186/s12859-016-0956-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/19/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND High-throughput RNA-Sequencing (RNA-Seq) has become the preferred technique for studying gene expression differences between biological samples and for discovering novel isoforms, though the techniques to analyze the resulting data are still immature. One pre-processing step that is widely but heterogeneously applied is trimming, in which low quality bases, identified by the probability that they are called incorrectly, are removed. However, the impact of trimming on subsequent alignment to a genome could influence downstream analyses including gene expression estimation; we hypothesized that this might occur in an inconsistent manner across different genes, resulting in differential bias. RESULTS To assess the effects of trimming on gene expression, we generated RNA-Seq data sets from four samples of larval Drosophila melanogaster sensory neurons, and used three trimming algorithms--SolexaQA, Trimmomatic, and ConDeTri-to perform quality-based trimming across a wide range of stringencies. After aligning the reads to the D. melanogaster genome with TopHat2, we used Cuffdiff2 to compare the original, untrimmed gene expression estimates to those following trimming. With the most aggressive trimming parameters, over ten percent of genes had significant changes in their estimated expression levels. This trend was seen with two additional RNA-Seq data sets and with alternative differential expression analysis pipelines. We found that the majority of the expression changes could be mitigated by imposing a minimum length filter following trimming, suggesting that the differential gene expression was primarily being driven by spurious mapping of short reads. Slight differences with the untrimmed data set remained after length filtering, which were associated with genes with low exon numbers and high GC content. Finally, an analysis of paired RNA-seq/microarray data sets suggests that no or modest trimming results in the most biologically accurate gene expression estimates. CONCLUSIONS We find that aggressive quality-based trimming has a large impact on the apparent makeup of RNA-Seq-based gene expression estimates, and that short reads can have a particularly strong impact. We conclude that implementation of trimming in RNA-Seq analysis workflows warrants caution, and if used, should be used in conjunction with a minimum read length filter to minimize the introduction of unpredictable changes in expression estimates.
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44
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Heckscher ES, Zarin AA, Faumont S, Clark MQ, Manning L, Fushiki A, Schneider-Mizell CM, Fetter RD, Truman JW, Zwart MF, Landgraf M, Cardona A, Lockery SR, Doe CQ. Even-Skipped(+) Interneurons Are Core Components of a Sensorimotor Circuit that Maintains Left-Right Symmetric Muscle Contraction Amplitude. Neuron 2015; 88:314-29. [PMID: 26439528 PMCID: PMC4619170 DOI: 10.1016/j.neuron.2015.09.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 07/30/2015] [Accepted: 09/02/2015] [Indexed: 11/16/2022]
Abstract
Bilaterally symmetric motor patterns--those in which left-right pairs of muscles contract synchronously and with equal amplitude (such as breathing, smiling, whisking, and locomotion)--are widespread throughout the animal kingdom. Yet, surprisingly little is known about the underlying neural circuits. We performed a thermogenetic screen to identify neurons required for bilaterally symmetric locomotion in Drosophila larvae and identified the evolutionarily conserved Even-skipped(+) interneurons (Eve/Evx). Activation or ablation of Eve(+) interneurons disrupted bilaterally symmetric muscle contraction amplitude, without affecting the timing of motor output. Eve(+) interneurons are not rhythmically active and thus function independently of the locomotor CPG. GCaMP6 calcium imaging of Eve(+) interneurons in freely moving larvae showed left-right asymmetric activation that correlated with larval behavior. TEM reconstruction of Eve(+) interneuron inputs and outputs showed that the Eve(+) interneurons are at the core of a sensorimotor circuit capable of detecting and modifying body wall muscle contraction.
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Affiliation(s)
- Ellie S Heckscher
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA; Howard Hughes Medical Institute, University of Oregon, Eugene, OR 97403, USA.
| | - Aref Arzan Zarin
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA; Howard Hughes Medical Institute, University of Oregon, Eugene, OR 97403, USA
| | - Serge Faumont
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Matthew Q Clark
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA; Howard Hughes Medical Institute, University of Oregon, Eugene, OR 97403, USA
| | - Laurina Manning
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA; Howard Hughes Medical Institute, University of Oregon, Eugene, OR 97403, USA
| | - Akira Fushiki
- Janelia Research Campus, HHMI, Ashburn, VA 20147, USA
| | | | | | | | - Maarten F Zwart
- Janelia Research Campus, HHMI, Ashburn, VA 20147, USA; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Matthias Landgraf
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | | | - Shawn R Lockery
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Chris Q Doe
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA; Howard Hughes Medical Institute, University of Oregon, Eugene, OR 97403, USA.
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