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Nourollah AM, Hassanpour H, Zehtabian A. Quantifying morphologies of developing neuronal cells using deep learning with imperfect annotations. IBRO Neurosci Rep 2024; 16:118-126. [PMID: 38282758 PMCID: PMC10820797 DOI: 10.1016/j.ibneur.2023.12.009] [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: 09/26/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024] Open
Abstract
The functionality of human intelligence relies on the interaction and health of neurons, hence, quantifying neuronal morphologies can be crucial for investigating the functionality of the human brain. This paper proposes a deep learning (DL) based method for segmenting and quantifying neuronal structures in fluorescence microscopy images of developing neuronal cells cultured in vitro. Compared to the majority of supervised DL-based segmentation methods that heavily rely on creating exact corresponding masks of neuronal structures for the preparation of training samples, the proposed approach allows for imperfect annotation of neurons, as it only requires tracing the centrelines of the neurites. This ability accelerates the preparation of training data by several folds. Our proposed framework is built on a modified version of PSPNet with an EfficientNet backbone pre-trained on the CityScapes dataset. To handle the imperfectness of training samples, we incorporated a weighted combination of two loss functions, namely the Dice loss and Lovász loss functions, into our network. We evaluated the proposed framework and several other state-of-the-art methods on a published dataset of approximately 900 manually quantified cultured mouse neurons. Our results indicate a close correlation between the proposed method and manual quantification in terms of neuron length and the number of branches while demonstrating improved analysis speed. Furthermore, the proposed method achieved high accuracy in neuron segmentation, as evidenced by the evaluation of the neurons' length and number of branches.
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Affiliation(s)
- Amir Masoud Nourollah
- Department of Computer Engineering and Information Technology, Shahrood University of Technology, Iran
| | - Hamid Hassanpour
- Department of Computer Engineering and Information Technology, Shahrood University of Technology, Iran
| | - Amin Zehtabian
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Germany
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2
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Li JH, Trivedi V, Diz-Muñoz A. Understanding the interplay of membrane trafficking, cell surface mechanics, and stem cell differentiation. Semin Cell Dev Biol 2023; 133:123-134. [PMID: 35641408 PMCID: PMC9703995 DOI: 10.1016/j.semcdb.2022.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/08/2022] [Accepted: 05/14/2022] [Indexed: 01/17/2023]
Abstract
Stem cells can generate a diversity of cell types during development, regeneration and adult tissue homeostasis. Differentiation changes not only the cell fate in terms of gene expression but also the physical properties and functions of cells, e.g. the secretory activity, cell shape, or mechanics. Conversely, these activities and properties can also regulate differentiation itself. Membrane trafficking is known to modulate signal transduction and thus has the potential to control stem cell differentiation. On the other hand, membrane trafficking, particularly from and to the plasma membrane, depends on the mechanical properties of the cell surface such as tension within the plasma membrane or the cortex. Indeed, recent findings demonstrate that cell surface mechanics can also control cell fate. Here, we review the bidirectional relationships between these three fundamental cellular functions, i.e. membrane trafficking, cell surface mechanics, and stem cell differentiation. Furthermore, we discuss commonly used methods in each field and how combining them with new tools will enhance our understanding of their interplay. Understanding how membrane trafficking and cell surface mechanics can guide stem cell fate holds great potential as these concepts could be exploited for directed differentiation of stem cells for the fields of tissue engineering and regenerative medicine.
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Affiliation(s)
- Jia Hui Li
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Vikas Trivedi
- EMBL, PRBB, Dr. Aiguader, 88, Barcelona 08003, Spain,Developmental Biology Unit, EMBL, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Alba Diz-Muñoz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, Heidelberg 69117, Germany.
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3
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Mekhaeil M, Dev KK, Conroy MJ. Existing Evidence for the Repurposing of PARP-1 Inhibitors in Rare Demyelinating Diseases. Cancers (Basel) 2022; 14:cancers14030687. [PMID: 35158955 PMCID: PMC8833351 DOI: 10.3390/cancers14030687] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/23/2022] [Accepted: 01/27/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Poly (ADP-ribose) polymerase-1 (PARP-1) inhibitors are successful cancer therapeutics that impair DNA repair machinery, leading to an accumulation of DNA damage and consequently cell death. The shared underlying mechanisms driving malignancy and demyelinating disease, together with the success of anticancer drugs as repurposed therapeutics, makes the repurposing of PARP-1 inhibitors for demyelinating diseases a worthy concept to consider. In addition, PARP-1 inhibitors demonstrate notable neuroprotective effects in demyelinating disorders, including multiple sclerosis which is considered the archetypical demyelinating disease. Abstract Over the past decade, Poly (ADP-ribose) polymerase-1 (PARP-1) inhibitors have arisen as a novel and promising targeted therapy for breast cancer gene (BRCA)-mutated ovarian and breast cancer patients. Therapies targeting the enzyme, PARP-1, have since established their place as maintenance drugs for cancer. Here, we present existing evidence that implicates PARP-1 as a player in the development and progression of both malignancy and demyelinating disease. These findings, together with the proven clinical efficacy and marketed success of PARP-1 inhibitors in cancer, present the repurposing of these drugs for demyelinating diseases as a desirable therapeutic concept. Indeed, PARP-1 inhibitors are noted to demonstrate neuroprotective effects in demyelinating disorders such as multiple sclerosis and Parkinson’s disease, further supporting the use of these drugs in demyelinating, neuroinflammatory, and neurodegenerative diseases. In this review, we discuss the potential for repurposing PARP-1 inhibitors, with a focus on rare demyelinating diseases. In particular, we address the possible use of PARP-1 inhibitors in examples of rare leukodystrophies, for which there are a paucity of treatment options and an urgent need for novel therapeutic approaches.
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Affiliation(s)
- Marianna Mekhaeil
- Drug Development Research Group, Department of Physiology, School of Medicine, Trinity College Dublin, D18 DH50 Dublin, Ireland; (M.M.); (K.K.D.)
- Cancer Immunology Research Group, Department of Physiology, School of Medicine, Trinity College Dublin, D18 DH50 Dublin, Ireland
| | - Kumlesh Kumar Dev
- Drug Development Research Group, Department of Physiology, School of Medicine, Trinity College Dublin, D18 DH50 Dublin, Ireland; (M.M.); (K.K.D.)
| | - Melissa Jane Conroy
- Cancer Immunology Research Group, Department of Physiology, School of Medicine, Trinity College Dublin, D18 DH50 Dublin, Ireland
- Correspondence:
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4
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Kind E, Longden KD, Nern A, Zhao A, Sancer G, Flynn MA, Laughland CW, Gezahegn B, Ludwig HDF, Thomson AG, Obrusnik T, Alarcón PG, Dionne H, Bock DD, Rubin GM, Reiser MB, Wernet MF. Synaptic targets of photoreceptors specialized to detect color and skylight polarization in Drosophila. eLife 2021; 10:e71858. [PMID: 34913436 PMCID: PMC8789284 DOI: 10.7554/elife.71858] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/15/2021] [Indexed: 11/18/2022] Open
Abstract
Color and polarization provide complementary information about the world and are detected by specialized photoreceptors. However, the downstream neural circuits that process these distinct modalities are incompletely understood in any animal. Using electron microscopy, we have systematically reconstructed the synaptic targets of the photoreceptors specialized to detect color and skylight polarization in Drosophila, and we have used light microscopy to confirm many of our findings. We identified known and novel downstream targets that are selective for different wavelengths or polarized light, and followed their projections to other areas in the optic lobes and the central brain. Our results revealed many synapses along the photoreceptor axons between brain regions, new pathways in the optic lobes, and spatially segregated projections to central brain regions. Strikingly, photoreceptors in the polarization-sensitive dorsal rim area target fewer cell types, and lack strong connections to the lobula, a neuropil involved in color processing. Our reconstruction identifies shared wiring and modality-specific specializations for color and polarization vision, and provides a comprehensive view of the first steps of the pathways processing color and polarized light inputs.
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Affiliation(s)
- Emil Kind
- Instititut für Biologie – Abteilung Neurobiologie, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität BerlinBerlinGermany
| | - Kit D Longden
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Aljoscha Nern
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Arthur Zhao
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Gizem Sancer
- Instititut für Biologie – Abteilung Neurobiologie, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität BerlinBerlinGermany
| | - Miriam A Flynn
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Connor W Laughland
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Bruck Gezahegn
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Henrique DF Ludwig
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Alex G Thomson
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Tessa Obrusnik
- Instititut für Biologie – Abteilung Neurobiologie, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität BerlinBerlinGermany
| | - Paula G Alarcón
- Instititut für Biologie – Abteilung Neurobiologie, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität BerlinBerlinGermany
| | - Heather Dionne
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Davi D Bock
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Gerald M Rubin
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Michael B Reiser
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Mathias F Wernet
- Instititut für Biologie – Abteilung Neurobiologie, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität BerlinBerlinGermany
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5
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Sancer G, Wernet MF. The development and function of neuronal subtypes processing color and skylight polarization in the optic lobes of Drosophila melanogaster. ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 61:101012. [PMID: 33618155 DOI: 10.1016/j.asd.2020.101012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 11/01/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
The retinal mosaics of many insects contain different ommatidial subtypes harboring photoreceptors that are both molecularly and morphologically specialized for comparing between different wavelengths versus detecting the orientation of skylight polarization. The neural circuits underlying these different inputs and the characterization of their specific cellular elements are the subject of intense research. Here we review recent progress on the description of both assembly and function of color and skylight polarization circuitry, by focusing on two cell types located in the distal portion of the medulla neuropil of the fruit fly Drosophila melanogaster's optic lobes, called Dm8 and Dm9. In the main part of the retina, Dm8 cells fall into two molecularly distinct subtypes whose center becomes specifically connected to either one of randomly distributed 'pale' or 'yellow' R7 photoreceptor fates during development. Only in the 'dorsal rim area' (DRA), both polarization-sensitive R7 and R8 photoreceptors are connected to different Dm8-like cell types, called Dm-DRA1 and Dm-DRA2, respectively. An additional layer of interommatidial integration is introduced by Dm9 cells, which receive input from multiple neighboring R7 and R8 cells, as well as providing feedback synapses back into these photoreceptors. As a result, the response properties of color-sensitive photoreceptor terminals are sculpted towards being both maximally decorrelated, as well as harboring several levels of opponency (both columnar as well as intercolumnar). In the DRA, individual Dm9 cells appear to mix both polarization and color signals, thereby potentially serving as the first level of integration of different celestial stimuli. The molecular mechanisms underlying the establishment of these synaptic connections are beginning to be revealed, by using a combination of live imaging, developmental genetic studies, and cell type-specific transcriptomics.
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Affiliation(s)
- Gizem Sancer
- Freie Universität Berlin, Fachbereich Biologie, Chemie und Pharmazie, Institut für Biologie - Neurobiologie, Königin-Luise Strasse 1-3, 14195 Berlin, Germany
| | - Mathias F Wernet
- Freie Universität Berlin, Fachbereich Biologie, Chemie und Pharmazie, Institut für Biologie - Neurobiologie, Königin-Luise Strasse 1-3, 14195 Berlin, Germany.
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6
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Impedance Measures and a Mounting Technique for Drosophila: Larval Movements, Heart Rate, Imaging, and Electrophysiology. Methods Protoc 2020; 3:mps3010012. [PMID: 31991683 PMCID: PMC7189670 DOI: 10.3390/mps3010012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/19/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
Monitoring movements of larval Drosophila with electrical detection allows one to record the behaviors without the use of lights and cameras. This is a suitable technique when studying the use of light-sensitive proteins in optogenetic studies. Electrical measures are feasible to use in determining when a larva starts to move or continues to move after a light induced activation of channelrhodopsin. We have developed a technique using an electrical measure of the media as an index of larval movement. As a proof of concept, recordings with an infrared camera of the larval movement were simultaneous made with electrical measures. The two techniques parallel each other in their ability to index larval movements. Bright light-emitting diode (LED) lights used in optogenetic experiments tend to saturate the detectors of the camera unless filters are used and different filters maybe necessary depending on the LED spectrum and sensitivity of the camera. Impedance measures are independent of the type of LED or brightness. We also assessed the use of a non-solvent based glue (3M Vetbond) to hold larvae in place while measuring synaptic function of neuromuscular junctions, cardiac function and influence of modulators, or activation of light-sensitive channels.
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7
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Cellular and synaptic adaptations of neural circuits processing skylight polarization in the fly. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2019; 206:233-246. [DOI: 10.1007/s00359-019-01389-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 10/25/2022]
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8
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Horne JA, Langille C, McLin S, Wiederman M, Lu Z, Xu CS, Plaza SM, Scheffer LK, Hess HF, Meinertzhagen IA. A resource for the Drosophila antennal lobe provided by the connectome of glomerulus VA1v. eLife 2018; 7:e37550. [PMID: 30382940 PMCID: PMC6234030 DOI: 10.7554/elife.37550] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 10/31/2018] [Indexed: 02/06/2023] Open
Abstract
Using FIB-SEM we report the entire synaptic connectome of glomerulus VA1v of the right antennal lobe in Drosophila melanogaster. Within the glomerulus we densely reconstructed all neurons, including hitherto elusive local interneurons. The fruitless-positive, sexually dimorphic VA1v included >11,140 presynaptic sites with ~38,050 postsynaptic dendrites. These connected input olfactory receptor neurons (ORNs, 51 ipsilateral, 56 contralateral), output projection neurons (18 PNs), and local interneurons (56 of >150 previously reported LNs). ORNs are predominantly presynaptic and PNs predominantly postsynaptic; newly reported LN circuits are largely an equal mixture and confer extensive synaptic reciprocity, except the newly reported LN2V with input from ORNs and outputs mostly to monoglomerular PNs, however. PNs were more numerous than previously reported from genetic screens, suggesting that the latter failed to reach saturation. We report a matrix of 192 bodies each having >50 connections; these form 88% of the glomerulus' pre/postsynaptic sites.
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Affiliation(s)
- Jane Anne Horne
- Department of Psychology and NeuroscienceLife Sciences Centre, Dalhousie UniversityHalifaxCanada
| | - Carlie Langille
- Department of Psychology and NeuroscienceLife Sciences Centre, Dalhousie UniversityHalifaxCanada
| | - Sari McLin
- Department of Psychology and NeuroscienceLife Sciences Centre, Dalhousie UniversityHalifaxCanada
| | - Meagan Wiederman
- Department of Psychology and NeuroscienceLife Sciences Centre, Dalhousie UniversityHalifaxCanada
| | - Zhiyuan Lu
- Department of Psychology and NeuroscienceLife Sciences Centre, Dalhousie UniversityHalifaxCanada
- Janelia Research Campus, Howard Hughes Medical InstituteVirginiaUnited States
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical InstituteVirginiaUnited States
| | - Stephen M Plaza
- Janelia Research Campus, Howard Hughes Medical InstituteVirginiaUnited States
| | - Louis K Scheffer
- Janelia Research Campus, Howard Hughes Medical InstituteVirginiaUnited States
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical InstituteVirginiaUnited States
| | - Ian A Meinertzhagen
- Department of Psychology and NeuroscienceLife Sciences Centre, Dalhousie UniversityHalifaxCanada
- Janelia Research Campus, Howard Hughes Medical InstituteVirginiaUnited States
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9
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Abstract
In general, neurons in insects and many other invertebrate groups are individually recognizable, enabling us to assign an index number to specific neurons in a manner which is rarely possible in a vertebrate brain. This endows many studies on insect nervous systems with the opportunity to document neurons with great precision, so that in favourable cases we can return to the same neuron or neuron type repeatedly so as to recognize many separate morphological classes. The visual system of the fly's compound eye particularly provides clear examples of the accuracy of neuron wiring, allowing numerical comparisons between representatives of the same cell type, and estimates of the accuracy of their wiring.
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Affiliation(s)
- Ian A Meinertzhagen
- a Department of Psychology and Neuroscience , Life Sciences Centre, Dalhousie University , Halifax , Canada.,b Janelia Research Campus of Howard Hughes Medical Institute , Ashburn , VA , USA
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10
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Heinloth T, Uhlhorn J, Wernet MF. Insect Responses to Linearly Polarized Reflections: Orphan Behaviors Without Neural Circuits. Front Cell Neurosci 2018; 12:50. [PMID: 29615868 PMCID: PMC5870057 DOI: 10.3389/fncel.2018.00050] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 02/15/2018] [Indexed: 12/13/2022] Open
Abstract
The e-vector orientation of linearly polarized light represents an important visual stimulus for many insects. Especially the detection of polarized skylight by many navigating insect species is known to improve their orientation skills. While great progress has been made towards describing both the anatomy and function of neural circuit elements mediating behaviors related to navigation, relatively little is known about how insects perceive non-celestial polarized light stimuli, like reflections off water, leaves, or shiny body surfaces. Work on different species suggests that these behaviors are not mediated by the “Dorsal Rim Area” (DRA), a specialized region in the dorsal periphery of the adult compound eye, where ommatidia contain highly polarization-sensitive photoreceptor cells whose receptive fields point towards the sky. So far, only few cases of polarization-sensitive photoreceptors have been described in the ventral periphery of the insect retina. Furthermore, both the structure and function of those neural circuits connecting to these photoreceptor inputs remain largely uncharacterized. Here we review the known data on non-celestial polarization vision from different insect species (dragonflies, butterflies, beetles, bugs and flies) and present three well-characterized examples for functionally specialized non-DRA detectors from different insects that seem perfectly suited for mediating such behaviors. Finally, using recent advances from circuit dissection in Drosophila melanogaster, we discuss what types of potential candidate neurons could be involved in forming the underlying neural circuitry mediating non-celestial polarization vision.
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Affiliation(s)
- Tanja Heinloth
- Division of Neurobiology, Institut für Biology, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität Berlin, Berlin, Germany
| | - Juliane Uhlhorn
- Division of Neurobiology, Institut für Biology, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität Berlin, Berlin, Germany
| | - Mathias F Wernet
- Division of Neurobiology, Institut für Biology, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität Berlin, Berlin, Germany
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11
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Panser K, Tirian L, Schulze F, Villalba S, Jefferis GSXE, Bühler K, Straw AD. Automatic Segmentation of Drosophila Neural Compartments Using GAL4 Expression Data Reveals Novel Visual Pathways. Curr Biol 2016; 26:1943-1954. [PMID: 27426516 PMCID: PMC4985560 DOI: 10.1016/j.cub.2016.05.052] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 04/14/2016] [Accepted: 05/20/2016] [Indexed: 01/26/2023]
Abstract
Identifying distinct anatomical structures within the brain and developing genetic tools to target them are fundamental steps for understanding brain function. We hypothesize that enhancer expression patterns can be used to automatically identify functional units such as neuropils and fiber tracts. We used two recent, genome-scale Drosophila GAL4 libraries and associated confocal image datasets to segment large brain regions into smaller subvolumes. Our results (available at https://strawlab.org/braincode) support this hypothesis because regions with well-known anatomy, namely the antennal lobes and central complex, were automatically segmented into familiar compartments. The basis for the structural assignment is clustering of voxels based on patterns of enhancer expression. These initial clusters are agglomerated to make hierarchical predictions of structure. We applied the algorithm to central brain regions receiving input from the optic lobes. Based on the automated segmentation and manual validation, we can identify and provide promising driver lines for 11 previously identified and 14 novel types of visual projection neurons and their associated optic glomeruli. The same strategy can be used in other brain regions and likely other species, including vertebrates. Genome-scale enhancer expression patterns can be used to predict brain structure Automated clustering of images finds known structures such as olfactory glomeruli Results identify GAL4 lines with strong expression in the predicted structures We validate novel predictions to reveal previously undescribed optic glomeruli
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Affiliation(s)
- Karin Panser
- Research Institute of Molecular Pathology (IMP), Vienna Bio-Center, Doktor-Bohr-Gasse 7, 1030 Vienna, Austria
| | - Laszlo Tirian
- Research Institute of Molecular Pathology (IMP), Vienna Bio-Center, Doktor-Bohr-Gasse 7, 1030 Vienna, Austria
| | - Florian Schulze
- VRVis Zentrum für Virtual Reality und Visualisierung Forschungs, Donau-City-Strasse 1, 1220 Vienna, Austria
| | - Santiago Villalba
- Research Institute of Molecular Pathology (IMP), Vienna Bio-Center, Doktor-Bohr-Gasse 7, 1030 Vienna, Austria
| | - Gregory S X E Jefferis
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Katja Bühler
- VRVis Zentrum für Virtual Reality und Visualisierung Forschungs, Donau-City-Strasse 1, 1220 Vienna, Austria
| | - Andrew D Straw
- Research Institute of Molecular Pathology (IMP), Vienna Bio-Center, Doktor-Bohr-Gasse 7, 1030 Vienna, Austria; Department of Neurobiology and Behavior, Institute of Biology I, University of Freiburg, Hauptstrasse 1, 79104 Freiburg, Germany.
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12
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Abstract
How stem cells produce the huge diversity of neurons that form the visual system, and how these cells are assembled in neural circuits are a critical question in developmental neurobiology. Investigations in Drosophila have led to the discovery of several basic principles of neural patterning. In this chapter, we provide an overview of the field by describing the development of the Drosophila visual system, from the embryo to the adult and from the gross anatomy to the cellular level. We then explore the general molecular mechanisms identified that might apply to other neural structures in flies or in vertebrates. Finally, we discuss the major challenges that remain to be addressed in the field.
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Affiliation(s)
- Nathalie Nériec
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE; Department of Biology, New York University, New York, USA
| | - Claude Desplan
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE; Department of Biology, New York University, New York, USA.
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13
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Li Y, Kilian KA. Bridging the Gap: From 2D Cell Culture to 3D Microengineered Extracellular Matrices. Adv Healthc Mater 2015; 4:2780-96. [PMID: 26592366 PMCID: PMC4780579 DOI: 10.1002/adhm.201500427] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/05/2015] [Indexed: 12/20/2022]
Abstract
Historically the culture of mammalian cells in the laboratory has been performed on planar substrates with media cocktails that are optimized to maintain phenotype. However, it is becoming increasingly clear that much of biology discerned from 2D studies does not translate well to the 3D microenvironment. Over the last several decades, 2D and 3D microengineering approaches have been developed that better recapitulate the complex architecture and properties of in vivo tissue. Inspired by the infrastructure of the microelectronics industry, lithographic patterning approaches have taken center stage because of the ease in which cell-sized features can be engineered on surfaces and within a broad range of biocompatible materials. Patterning and templating techniques enable precise control over extracellular matrix properties including: composition, mechanics, geometry, cell-cell contact, and diffusion. In this review article we explore how the field of engineered extracellular matrices has evolved with the development of new hydrogel chemistry and the maturation of micro- and nano- fabrication. Guided by the spatiotemporal regulation of cell state in developing tissues, techniques for micropatterning in 2D, pseudo-3D systems, and patterning within 3D hydrogels will be discussed in the context of translating the information gained from 2D systems to synthetic engineered 3D tissues.
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Affiliation(s)
- Yanfen Li
- Department of Materials Science and Engineering, Department of Bioengineering, Institute for Genomic Biology, Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana IL, 61801
| | - Kristopher A. Kilian
- Department of Materials Science and Engineering, Department of Bioengineering, Institute for Genomic Biology, Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana IL, 61801
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14
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Structural Components of Synaptic Plasticity and Memory Consolidation. Cold Spring Harb Perspect Biol 2015; 7:a021758. [PMID: 26134321 DOI: 10.1101/cshperspect.a021758] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Consolidation of implicit memory in the invertebrate Aplysia and explicit memory in the mammalian hippocampus are associated with remodeling and growth of preexisting synapses and the formation of new synapses. Here, we compare and contrast structural components of the synaptic plasticity that underlies these two distinct forms of memory. In both cases, the structural changes involve time-dependent processes. Thus, some modifications are transient and may contribute to early formative stages of long-term memory, whereas others are more stable, longer lasting, and likely to confer persistence to memory storage. In addition, we explore the possibility that trans-synaptic signaling mechanisms governing de novo synapse formation during development can be reused in the adult for the purposes of structural synaptic plasticity and memory storage. Finally, we discuss how these mechanisms set in motion structural rearrangements that prepare a synapse to strengthen the same memory and, perhaps, to allow it to take part in other memories as a basis for understanding how their anatomical representation results in the enhanced expression and storage of memories in the brain.
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15
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Silvestri L, Paciscopi M, Soda P, Biamonte F, Iannello G, Frasconi P, Pavone FS. Quantitative neuroanatomy of all Purkinje cells with light sheet microscopy and high-throughput image analysis. Front Neuroanat 2015; 9:68. [PMID: 26074783 PMCID: PMC4445386 DOI: 10.3389/fnana.2015.00068] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/11/2015] [Indexed: 02/02/2023] Open
Abstract
Characterizing the cytoarchitecture of mammalian central nervous system on a brain-wide scale is becoming a compelling need in neuroscience. For example, realistic modeling of brain activity requires the definition of quantitative features of large neuronal populations in the whole brain. Quantitative anatomical maps will also be crucial to classify the cytoarchtitectonic abnormalities associated with neuronal pathologies in a high reproducible and reliable manner. In this paper, we apply recent advances in optical microscopy and image analysis to characterize the spatial distribution of Purkinje cells (PCs) across the whole cerebellum. Light sheet microscopy was used to image with micron-scale resolution a fixed and cleared cerebellum of an L7-GFP transgenic mouse, in which all PCs are fluorescently labeled. A fast and scalable algorithm for fully automated cell identification was applied on the image to extract the position of all the fluorescent PCs. This vectorized representation of the cell population allows a thorough characterization of the complex three-dimensional distribution of the neurons, highlighting the presence of gaps inside the lamellar organization of PCs, whose density is believed to play a significant role in autism spectrum disorders. Furthermore, clustering analysis of the localized somata permits dividing the whole cerebellum in groups of PCs with high spatial correlation, suggesting new possibilities of anatomical partition. The quantitative approach presented here can be extended to study the distribution of different types of cell in many brain regions and across the whole encephalon, providing a robust base for building realistic computational models of the brain, and for unbiased morphological tissue screening in presence of pathologies and/or drug treatments.
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Affiliation(s)
- Ludovico Silvestri
- National Institute of Optics, National Research Council Sesto Fiorentino, Italy ; European Laboratory for Non-Linear Spectroscopy Sesto Fiorentino, Italy
| | - Marco Paciscopi
- Department of Information Engineering, University of Florence Florence, Italy
| | - Paolo Soda
- Department of Engineering, University Campus Bio-Medico of Rome Rome, Italy
| | - Filippo Biamonte
- Institute of Histology and Embryology, Catholic University of the Sacred Heart "A. Gemelli", Rome Italy
| | - Giulio Iannello
- Department of Engineering, University Campus Bio-Medico of Rome Rome, Italy
| | - Paolo Frasconi
- European Laboratory for Non-Linear Spectroscopy Sesto Fiorentino, Italy
| | - Francesco S Pavone
- National Institute of Optics, National Research Council Sesto Fiorentino, Italy ; European Laboratory for Non-Linear Spectroscopy Sesto Fiorentino, Italy ; Department of Physics and Astronomy, University of Florence Sesto Fiorentino, Italy ; International Center for Computational Neurophotonics Sesto Fiorentino, Italy
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Wernet MF, Huberman AD, Desplan C. So many pieces, one puzzle: cell type specification and visual circuitry in flies and mice. Genes Dev 2014; 28:2565-84. [PMID: 25452270 PMCID: PMC4248288 DOI: 10.1101/gad.248245.114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The visual system is a powerful model for probing the development, connectivity, and function of neural circuits. Two genetically tractable species, mice and flies, are together providing a great deal of understanding of these processes. Current efforts focus on integrating knowledge gained from three cross-fostering fields of research: (1) understanding how the fates of different cell types are specified during development, (2) revealing the synaptic connections between identified cell types ("connectomics") by high-resolution three-dimensional circuit anatomy, and (3) causal testing of how identified circuit elements contribute to visual perception and behavior. Here we discuss representative examples from fly and mouse models to illustrate the ongoing success of this tripartite strategy, focusing on the ways it is enhancing our understanding of visual processing and other sensory systems.
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Affiliation(s)
- Mathias F Wernet
- Department of Neurobiology, Stanford University, Stanford, California 94305, USA; New York University Abu Dhabi, Saadiyat Island, Abu Dhabi 129188, United Arab Emirates; Department of Biology, New York University, New York, New York 10003, USA
| | - Andrew D Huberman
- Department of Neurosciences, Neurobiology Section, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093, USA
| | - Claude Desplan
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi 129188, United Arab Emirates; Department of Biology, New York University, New York, New York 10003, USA
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17
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Flow cytometry analysis of synaptosomes from post-mortem human brain reveals changes specific to Lewy body and Alzheimer's disease. J Transl Med 2014; 94:1161-72. [PMID: 25068655 PMCID: PMC4184945 DOI: 10.1038/labinvest.2014.103] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 06/10/2014] [Accepted: 06/13/2014] [Indexed: 01/25/2023] Open
Abstract
Synaptic dysfunction is thought to have an important role in the pathophysiology of neurodegenerative diseases, such as Alzheimer's disease (AD) and Lewy body disease (LBD). To improve our understanding of synaptic alterations in health and disease, we investigated synaptosomes prepared from post-mortem human cerebral cortex, putamen (PT), and two regions of the caudate nucleus, dorso-lateral (DL) and ventro-medial (VM), regions commonly affected in AD and LBD. We observed that the fraction of synaptosomal particles with reactivity for dopamine transporter (DAT) was significantly reduced in the PT and VM caudate of patients with neuropathological diagnosis of LBD. As expected, these differences also were reflected in direct measurements of dopamine (DA) and its metabolite, 3,4-dihydroxyphenylacetic acid (DOPAC), in caudate and PT of LBD patients. The fraction of synaptosomal particles positive for amyloid β (Aβ) was significantly increased in frontal cortical samples of patients with the neuropathological diagnosis of severe AD, and was positively correlated with disease progression. We also prepared synaptosomes from the striatum of mice with severe loss of DA neurons (Slc6a3-DTR mice) and wild-type littermate controls. We observed markedly reduced levels of DAT-positive synaptosomes in Slc6a3-DTR mice following exposure to diphtheria toxin (DT). Striatal levels of DA and DOPAC in Slc6a3-DTR mice also were reduced significantly following DT exposure. We conclude that flow cytometric analysis of synaptosomes prepared from human or mouse brain provides an opportunity to study expression of pathology-associated proteins and also the specific loss of dopaminergic nerve terminals. Hence, we believe it is a valid method to detect pathological changes at the level of the synapse in LBD as well as AD.
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Abstract
The description of the Rst protein by Karl-Friedrich Fischbach and colleagues was a milestone in the discovery of the irre cell recognition module (IRM). IRM proteins represent a family of immunoglobulin superfamily cell adhesion proteins that orchestrate intercellular adhesion and signaling events necessary for the development of various tissues. This review briefly summarizes the fundamental role of IRM proteins for neuronal wiring and filtration in organisms spanning the evolutionary distance from Drosophila (nephrocyte diaphragm) to humans (slit diaphragm).
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19
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Abdus-Saboor I, Stone CE, Murray JI, Sundaram MV. The Nkx5/HMX homeodomain protein MLS-2 is required for proper tube cell shape in the C. elegans excretory system. Dev Biol 2012; 366:298-307. [PMID: 22537498 DOI: 10.1016/j.ydbio.2012.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/26/2012] [Accepted: 03/28/2012] [Indexed: 01/20/2023]
Abstract
Cells perform wide varieties of functions that are facilitated, in part, by adopting unique shapes. Many of the genes and pathways that promote cell fate specification have been elucidated. However, relatively few transcription factors have been identified that promote shape acquisition after fate specification. Here we show that the Nkx5/HMX homeodomain protein MLS-2 is required for cellular elongation and shape maintenance of two tubular epithelial cells in the C. elegans excretory system, the duct and pore cells. The Nkx5/HMX family is highly conserved from sea urchins to humans, with known roles in neuronal and glial development. MLS-2 is expressed in the duct and pore, and defects in mls-2 mutants first arise when the duct and pore normally adopt unique shapes. MLS-2 cooperates with the EGF-Ras-ERK pathway to turn on the LIN-48/Ovo transcription factor in the duct cell during morphogenesis. These results reveal a novel interaction between the Nkx5/HMX family and the EGF-Ras pathway and implicate a transcription factor, MLS-2, as a regulator of cell shape.
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Affiliation(s)
- Ishmail Abdus-Saboor
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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20
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Meinertzhagen IA, Lee CH. The genetic analysis of functional connectomics in Drosophila. ADVANCES IN GENETICS 2012; 80:99-151. [PMID: 23084874 DOI: 10.1016/b978-0-12-404742-6.00003-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fly and vertebrate nervous systems share many organizational features, such as layers, columns and glomeruli, and utilize similar synaptic components, such as ion channels and receptors. Both also exhibit similar network features. Recent technological advances, especially in electron microscopy, now allow us to determine synaptic circuits and identify pathways cell-by-cell, as part of the fly's connectome. Genetic tools provide the means to identify synaptic components, as well as to record and manipulate neuronal activity, adding function to the connectome. This review discusses technical advances in these emerging areas of functional connectomics, offering prognoses in each and identifying the challenges in bridging structural connectomics to molecular biology and synaptic physiology, thereby determining fundamental mechanisms of neural computation that underlie behavior.
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Affiliation(s)
- Ian A Meinertzhagen
- Department of Psychology and Neuroscience, Life Sciences Centre, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2.
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21
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Takemura SY, Karuppudurai T, Ting CY, Lu Z, Lee CH, Meinertzhagen IA. Cholinergic circuits integrate neighboring visual signals in a Drosophila motion detection pathway. Curr Biol 2011; 21:2077-84. [PMID: 22137471 PMCID: PMC3265035 DOI: 10.1016/j.cub.2011.10.053] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/20/2011] [Accepted: 10/31/2011] [Indexed: 11/21/2022]
Abstract
Detecting motion is a feature of all advanced visual systems [1], nowhere more so than in flying animals, like insects [2, 3]. In flies, an influential autocorrelation model for motion detection, the elementary motion detector circuit (EMD; [4, 5]), compares visual signals from neighboring photoreceptors to derive information on motion direction and velocity. This information is fed by two types of interneuron, L1 and L2, in the first optic neuropile, or lamina, to downstream local motion detectors in columns of the second neuropile, the medulla. Despite receiving carefully matched photoreceptor inputs, L1 and L2 drive distinct, separable pathways responding preferentially to moving "on" and "off" edges, respectively [6, 7]. Our serial electron microscopy (EM) identifies two types of transmedulla (Tm) target neurons, Tm1 and Tm2, that receive apparently matched synaptic inputs from L2. Tm2 neurons also receive inputs from two retinotopically posterior neighboring columns via L4, a third type of lamina neuron. Light microscopy reveals that the connections in these L2/L4/Tm2 circuits are highly determinate. Single-cell transcript profiling suggests that nicotinic acetylcholine receptors mediate transmission within the L2/L4/Tm2 circuits, whereas L1 is apparently glutamatergic. We propose that Tm2 integrates sign-conserving inputs from neighboring columns to mediate the detection of front-to-back motion generated during forward motion.
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MESH Headings
- Adaptation, Physiological
- Animals
- Drosophila melanogaster/cytology
- Drosophila melanogaster/metabolism
- Drosophila melanogaster/physiology
- Drosophila melanogaster/radiation effects
- Interneurons/physiology
- Microscopy, Electron
- Motion Perception
- Optic Lobe, Nonmammalian/cytology
- Optic Lobe, Nonmammalian/physiology
- Optic Lobe, Nonmammalian/radiation effects
- Photoreceptor Cells, Invertebrate/cytology
- Photoreceptor Cells, Invertebrate/metabolism
- Photoreceptor Cells, Invertebrate/radiation effects
- Receptors, Glutamate/physiology
- Receptors, Nicotinic/physiology
- Signal Transduction
- Vision, Ocular/physiology
- Vision, Ocular/radiation effects
- Visual Pathways/cytology
- Visual Pathways/physiology
- Visual Pathways/radiation effects
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Affiliation(s)
- Shin-ya Takemura
- Department of Psychology, Life Sciences Centre, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J1
- Department of Biology, Life Sciences Centre, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J1
| | - Thangavel Karuppudurai
- Section on Neuronal Connectivity, Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
| | - Chun-Yuan Ting
- Section on Neuronal Connectivity, Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
| | - Zhiyuan Lu
- Department of Psychology, Life Sciences Centre, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J1
| | - Chi-Hon Lee
- Section on Neuronal Connectivity, Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
| | - Ian A. Meinertzhagen
- Department of Psychology, Life Sciences Centre, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J1
- Department of Biology, Life Sciences Centre, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J1
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22
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Venken KJ, Simpson JH, Bellen HJ. Genetic manipulation of genes and cells in the nervous system of the fruit fly. Neuron 2011; 72:202-30. [PMID: 22017985 PMCID: PMC3232021 DOI: 10.1016/j.neuron.2011.09.021] [Citation(s) in RCA: 301] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2011] [Indexed: 12/26/2022]
Abstract
Research in the fruit fly Drosophila melanogaster has led to insights in neural development, axon guidance, ion channel function, synaptic transmission, learning and memory, diurnal rhythmicity, and neural disease that have had broad implications for neuroscience. Drosophila is currently the eukaryotic model organism that permits the most sophisticated in vivo manipulations to address the function of neurons and neuronally expressed genes. Here, we summarize many of the techniques that help assess the role of specific neurons by labeling, removing, or altering their activity. We also survey genetic manipulations to identify and characterize neural genes by mutation, overexpression, and protein labeling. Here, we attempt to acquaint the reader with available options and contexts to apply these methods.
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Affiliation(s)
- Koen J.T. Venken
- Department of Molecular and Human Genetics, Neurological Research Institute, Baylor College of Medicine, Houston, Texas, 77030
| | - Julie H. Simpson
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, 20147
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Neurological Research Institute, Baylor College of Medicine, Houston, Texas, 77030
- Program in Developmental Biology, Department of Neuroscience, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, 77030
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23
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Richter S, Loesel R, Purschke G, Schmidt-Rhaesa A, Scholtz G, Stach T, Vogt L, Wanninger A, Brenneis G, Döring C, Faller S, Fritsch M, Grobe P, Heuer CM, Kaul S, Møller OS, Müller CHG, Rieger V, Rothe BH, Stegner MEJ, Harzsch S. Invertebrate neurophylogeny: suggested terms and definitions for a neuroanatomical glossary. Front Zool 2010; 7:29. [PMID: 21062451 PMCID: PMC2996375 DOI: 10.1186/1742-9994-7-29] [Citation(s) in RCA: 232] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2010] [Accepted: 11/09/2010] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Invertebrate nervous systems are highly disparate between different taxa. This is reflected in the terminology used to describe them, which is very rich and often confusing. Even very general terms such as 'brain', 'nerve', and 'eye' have been used in various ways in the different animal groups, but no consensus on the exact meaning exists. This impedes our understanding of the architecture of the invertebrate nervous system in general and of evolutionary transformations of nervous system characters between different taxa. RESULTS We provide a glossary of invertebrate neuroanatomical terms with a precise and consistent terminology, taxon-independent and free of homology assumptions. This terminology is intended to form a basis for new morphological descriptions. A total of 47 terms are defined. Each entry consists of a definition, discouraged terms, and a background/comment section. CONCLUSIONS The use of our revised neuroanatomical terminology in any new descriptions of the anatomy of invertebrate nervous systems will improve the comparability of this organ system and its substructures between the various taxa, and finally even lead to better and more robust homology hypotheses.
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Affiliation(s)
- Stefan Richter
- Universität Rostock, Institut für Biowissenschaften, Abteilung für Allgemeine und Spezielle Zoologie, Universitätsplatz 2, D-18055 Rostock, Germany
| | - Rudi Loesel
- RWTH Aachen, Institute of Biology II, Department of Developmental Biology and Morphology of Animals, Mies-van-der-Rohe-Straße 15, D-52056 Aachen, Germany
| | - Günter Purschke
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Zoologie, Barbarastraße 11,, D-49069 Osnabrück, Germany
| | - Andreas Schmidt-Rhaesa
- Biozentrum Grindel/Zoological Museum, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
| | - Gerhard Scholtz
- Humboldt-Universität zu Berlin, Institut für Biologie - Vergleichende Zoologie, Philippstraße 13, D-10115 Berlin, Germany
| | - Thomas Stach
- Freie Universität Berlin, Zoologie - Systematik und Evolutionsforschung, Königin-Luise-Straße 1-3, D-14195 Berlin, Germany
| | - Lars Vogt
- Universität Bonn, Institut für Evolutionsbiologie und Ökologie, An der Immenburg 1, D-53121 Bonn, Germany
| | - Andreas Wanninger
- University of Copenhagen, Department of Biology, Research Group for Comparative Zoology, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Georg Brenneis
- Universität Rostock, Institut für Biowissenschaften, Abteilung für Allgemeine und Spezielle Zoologie, Universitätsplatz 2, D-18055 Rostock, Germany
- Humboldt-Universität zu Berlin, Institut für Biologie - Vergleichende Zoologie, Philippstraße 13, D-10115 Berlin, Germany
| | - Carmen Döring
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Zoologie, Barbarastraße 11,, D-49069 Osnabrück, Germany
| | - Simone Faller
- RWTH Aachen, Institute of Biology II, Department of Developmental Biology and Morphology of Animals, Mies-van-der-Rohe-Straße 15, D-52056 Aachen, Germany
| | - Martin Fritsch
- Universität Rostock, Institut für Biowissenschaften, Abteilung für Allgemeine und Spezielle Zoologie, Universitätsplatz 2, D-18055 Rostock, Germany
| | - Peter Grobe
- Universität Bonn, Institut für Evolutionsbiologie und Ökologie, An der Immenburg 1, D-53121 Bonn, Germany
| | - Carsten M Heuer
- RWTH Aachen, Institute of Biology II, Department of Developmental Biology and Morphology of Animals, Mies-van-der-Rohe-Straße 15, D-52056 Aachen, Germany
| | - Sabrina Kaul
- Freie Universität Berlin, Zoologie - Systematik und Evolutionsforschung, Königin-Luise-Straße 1-3, D-14195 Berlin, Germany
| | - Ole S Møller
- Universität Rostock, Institut für Biowissenschaften, Abteilung für Allgemeine und Spezielle Zoologie, Universitätsplatz 2, D-18055 Rostock, Germany
| | - Carsten HG Müller
- Ernst-Moritz-Arndt-Universität Greifswald, Zoologisches Institut, Cytologie und Evolutionsbiologie, Johann-Sebastian-Bach-Straße 11/12, D-17487 Greifswald, Germany
| | - Verena Rieger
- Ernst-Moritz-Arndt-Universität Greifswald, Zoologisches Institut, Cytologie und Evolutionsbiologie, Johann-Sebastian-Bach-Straße 11/12, D-17487 Greifswald, Germany
| | - Birgen H Rothe
- Biozentrum Grindel/Zoological Museum, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
| | - Martin EJ Stegner
- Universität Rostock, Institut für Biowissenschaften, Abteilung für Allgemeine und Spezielle Zoologie, Universitätsplatz 2, D-18055 Rostock, Germany
| | - Steffen Harzsch
- Ernst-Moritz-Arndt-Universität Greifswald, Zoologisches Institut, Cytologie und Evolutionsbiologie, Johann-Sebastian-Bach-Straße 11/12, D-17487 Greifswald, Germany
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24
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Chklovskii DB, Vitaladevuni S, Scheffer LK. Semi-automated reconstruction of neural circuits using electron microscopy. Curr Opin Neurobiol 2010; 20:667-75. [PMID: 20833533 DOI: 10.1016/j.conb.2010.08.002] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Accepted: 08/04/2010] [Indexed: 11/29/2022]
Abstract
Reconstructing neuronal circuits at the level of synapses is a central problem in neuroscience, and the focus of the nascent field of connectomics. Previously used to reconstruct the C. elegans wiring diagram, serial-section transmission electron microscopy (ssTEM) is a proven technique for the task. However, to reconstruct more complex circuits, ssTEM will require the automation of image processing. We review progress in the processing of electron microscopy images and, in particular, a semi-automated reconstruction pipeline deployed at Janelia Farm. Drosophila circuits underlying identified behaviors are being reconstructed in the pipeline with the goal of generating a complete Drosophila connectome.
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Affiliation(s)
- Dmitri B Chklovskii
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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25
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Mytilinaios DG, Tsamis KI, Njau SN, Polyzoides K, Baloyannis SJ. Neuropathological findings in Dandy Walker variant. Dev Neurorehabil 2010; 13:64-7. [PMID: 20067347 DOI: 10.3109/17518420903236254] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Dandy-Walker malformation is a congenital malformation that is characterized by hypoplasia of the cerebellar vermis, cystic dilatation of the fourth ventricle and enlargement of the posterior fossa. The aim of the study is to describe the morphological and morphometric alterations of neurons (in various regions of the brain) in a case of Dandy-Walker Variant. METHODS By Golgi method and routine techniques, the alterations in the brain of a 23 years old case of Dandy-Walker Variant who died accidentally were studied. Furthermore, a detailed morphometric analysis of neuronal parameters and a statistical comparison with an age-matched control were applied. RESULTS In the cerebellum the morphological study, apart from gliosis, revealed reduction of the size of cell body and poverty of dendritic arborization with loss of dendritic branches and spines. In the cerebral cortex and the hippocampus the most prominent findings were the tortuous configuration of the apical dendrites of the pyramidal neurons, the focal swellings of the axons and the dendrites and significant gliosis. CONCLUSION Although the gross anatomical examination of the brain demonstrated only mild neurodevelopmental anomalies (except the key features of the syndrome), the microscopic examination revealed significant morphological alterations of neurons and dendrites.
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