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McDougal RA, Conte C, Eggleston L, Newton AJH, Galijasevic H. Efficient Simulation of 3D Reaction-Diffusion in Models of Neurons and Networks. Front Neuroinform 2022; 16:847108. [PMID: 35655652 PMCID: PMC9152282 DOI: 10.3389/fninf.2022.847108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 04/20/2022] [Indexed: 12/20/2022] Open
Abstract
Neuronal activity is the result of both the electrophysiology and chemophysiology. A neuron can be well-represented for the purposes of electrophysiological simulation as a tree composed of connected cylinders. This representation is also apt for 1D simulations of their chemophysiology, provided the spatial scale is larger than the diameter of the cylinders and there is radial symmetry. Higher dimensional simulation is necessary to accurately capture the dynamics when these criteria are not met, such as with wave curvature, spines, or diffusion near the soma. We have developed a solution to enable efficient finite volume method simulation of reaction-diffusion kinetics in intracellular 3D regions in neuron and network models and provide an implementation within the NEURON simulator. An accelerated version of the CTNG 3D reconstruction algorithm transforms morphologies suitable for ion-channel based simulations into consistent 3D voxelized regions. Kinetics are then solved using a parallel algorithm based on Douglas-Gunn that handles the irregular 3D geometry of a neuron; these kinetics are coupled to NEURON's 1D mechanisms for ion channels, synapses, pumps, and so forth. The 3D domain may cover the entire cell or selected regions of interest. Simulations with dendritic spines and of the soma reveal details of dynamics that would be missed in a pure 1D simulation. We describe and validate the methods and discuss their performance.
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Affiliation(s)
- Robert A McDougal
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States.,Center for Medical Informatics, Yale University, New Haven, CT, United States.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Cameron Conte
- Center for Medical Informatics, Yale University, New Haven, CT, United States.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, United States.,Department of Statistics, The Ohio State University, Columbus, OH, United States
| | - Lia Eggleston
- Yale College, Yale University, New Haven, CT, United States
| | - Adam J H Newton
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States.,Center for Medical Informatics, Yale University, New Haven, CT, United States.,Department of Physiology and Pharmacology, SUNY Downstate Health Sciences University, New York, NY, United States
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Guimaraes BDPPF, Curado MR, Nogueira-Campos AA, Houzel JC, Gattass R. Nitrergic neurons of the forepaw representation in the rat somatosensory and motor cortices: A quantitative study. J Comp Neurol 2021; 529:3321-3335. [PMID: 34008863 DOI: 10.1002/cne.25192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 11/07/2022]
Abstract
Nitrergic neurons (NNs) are inhibitory neurons capable of releasing nitric oxide (NO) that are labeled with nicotinamide adenine dinucleotide phosphate diaphorase histochemistry. The rat primary somatosensory (S1) and motor (M1) cortices are a favorable model to investigate NN populations by comparing their morphology, since these areas share the border of forepaw representation. The distribution of the Type I NN of the forepaw representation in the S1 and M1 cortices of the rat in different laminar compartments and the morphological parameters related to the cell body and dendritic arborization were measured and compared. We observed that the neuronal density in the S1 (130 NN/mm3 ) was higher than the neuronal density in the M1 (119 NN/mm3 ). Most NN neurons were multipolar (S1 with 58%; M1 with 69%), and a minority of the NN neurons were horizontal (S1 with 6%; M1 with 12%). NN found in S1 had a higher verticality index than NN found in M1, and no significant differences were observed for the other morphological parameters. We also demonstrated significant differences in most of the morphological parameters of the NN between different cortical compartments of S1 and M1. Our results indicate that the NN of the forepaw in S1 and M1 corresponds to a neuronal population, where the functionality is independent of the different types of sensory and motor processing. However, the morphological differences found between the cortical compartments of S1 and M1, as well as the higher density of NNs found in S1, indicate that the release of NO varies between the areas.
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Affiliation(s)
| | - Marco Rocha Curado
- Program of Morphological Science, Institute of Biomedical Science, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anaelli Aparecida Nogueira-Campos
- Laboratory of Cognitive Neurophysiology, Department of Physiology, Institute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Jean Christophe Houzel
- Program of Morphological Science, Institute of Biomedical Science, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo Gattass
- Program of Neurobiology, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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3
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Friedman R. Measurements of neuronal morphological variation across the rat neocortex. Neurosci Lett 2020; 734:135077. [PMID: 32485285 DOI: 10.1016/j.neulet.2020.135077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/20/2020] [Indexed: 11/16/2022]
Abstract
Neuron morphology is highly variable across the mammalian brain. It is thought that these attributes of neuronal cell shape, such as soma surface area and branching frequency, are determined by biological function and information processing. In this study, a large data set of neurons across the rat neocortex were clustered by their anatomical characters for evidence of distinctiveness among neocortical regions and the somatosensory layers. This data set of neuronal morphologies was compiled from 31 different lab sources with a validation procedure so that data records are potentially comparable across research studies. With this large set of heterogeneous data and by clustering analysis, this study shows that neuronal morphological traits overlap among neocortical and somatosensory regions. In the context of past neuroanatomical studies, this result is not congruent with tissue level analysis and strongly suggests further sampling of neuronal data to lessen the effect of confounding factors, such as the influence of different methodologies from use of heterogeneous samples of neuronal data.
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Affiliation(s)
- Robert Friedman
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States.
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Almási Z, Dávid C, Witte M, Staiger JF. Distribution Patterns of Three Molecularly Defined Classes of GABAergic Neurons Across Columnar Compartments in Mouse Barrel Cortex. Front Neuroanat 2019; 13:45. [PMID: 31114486 PMCID: PMC6503091 DOI: 10.3389/fnana.2019.00045] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
The mouse somatosensory cortex is an excellent model to study the structural basis of cortical information processing, since it possesses anatomically recognizable domains that receive different thalamic inputs, which indicates spatial segregation of different processing tasks. In this work we examined three genetically labeled, non-overlapping subpopulations of GABAergic neurons: parvalbumin- (PV+), somatostatin- (SST+), and vasoactive intestinal polypeptide-expressing (VIP+) cells. Each of these subpopulations displayed a unique cellular distribution pattern across layers. In terms of columnar localization, the distribution of these three populations was not quantitatively different between barrel-related versus septal compartments in most layers. However, in layer IV (LIV), SST+, and VIP+, but not PV+ neurons preferred the septal compartment over barrels. The examined cell types showed a tendency toward differential distribution in supragranular and infragranular barrel-related versus septal compartments, too. Our data suggests that the location of GABAergic neuron cell bodies correlates with the spatial pattern of cortical domains receiving different kinds of thalamic input. Thus, at least in LIV, lemniscal inputs present a close spatial relation preferentially to PV+ cells whereas paralemniscal inputs target compartments in which more SST+ and VIP+ cells are localized. Our findings suggest pathway-specific roles for neocortical GABAergic neurons.
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Affiliation(s)
- Zsuzsanna Almási
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Csaba Dávid
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Mirko Witte
- Center Anatomy, Institute for Neuroanatomy, Georg-August-University Göttingen, Göttingen, Germany
| | - Jochen F. Staiger
- Center Anatomy, Institute for Neuroanatomy, Georg-August-University Göttingen, Göttingen, Germany
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Afarinesh MR, Behzadi G. The Effects of De-Whiskering and Congenital Hypothyroidism on The Development of Nitrergic Neurons in Rat Primary Somatosensory and Motor Cortices. CELL JOURNAL 2018; 20:157-167. [PMID: 29633592 PMCID: PMC5893286 DOI: 10.22074/cellj.2018.5112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 03/14/2017] [Indexed: 11/25/2022]
Abstract
Objective The aim of the present study is to investigate the effects of chronic whisker deprivation on possible alterations to
the development of nitrergic neurons in the whisker part of the somatosensory (wS1) and motor (wM1) cortices in offspring
with congenital hypothyroidism (CH).
Materials and Methods In the experimental study, CH was induced by adding propylthiouracil to the rats drinking water from
embryonic day 16 to postnatal day (PND) 60. In whisker-deprived (WD) pups, all the whiskers were trimmed from PND 1 to
60. Nitrergic interneurons in the wS1/M1 cortices were detected by NADPH-diaphorase histochemistry staining technique in
the control (Ctl), Ctl+WD, Hypo and Hypo+WD groups.
Results In both wS1 and wM1 cortices the number of nitrergic neurons was significantly reduced in the Hypo and
Hypo+WD groups compared to Ctl and Ctl+WD groups, respectively (P<0.05) while bilateral whisker deprivation had no
remarkable effect. The mean soma diameter size of NADPH-d labeled neurons in the Ctl+WD and Hypo+WD groups
was decreased compared to the Ctl and Hypo groups, respectively. A similar patterns of decreased NADPH-d labeled
neurons in the wS1/M1 cortices occur in the processes of nitrergic neurons in both congenital hypothyroidism and
whisker deprivation.
Conclusion Our results suggest that both congenital hypothyroidism and whisker deprivation may disturb normal
development of the wS1 and wM1 cortical circuits in which nitrergic neurons are involved.
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Affiliation(s)
- Mohammad Reza Afarinesh
- Isfahan Neuroscience Research Center (INRC), Alzahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Gila Behzadi
- Functional Neuroanatomy Labaratory, Department of Physiology, Faculty of Medicine, Shahid Beheshti Medicine Science University, Tehran, Iran
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Wang X, Liu C, Wang X, Gao F, Zhan RZ. Density and neurochemical profiles of neuronal nitric oxide synthase-expressing interneuron in the mouse basolateral amygdala. Brain Res 2017; 1663:106-113. [DOI: 10.1016/j.brainres.2017.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 12/24/2016] [Accepted: 02/12/2017] [Indexed: 01/28/2023]
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Nanda S, Allaham MM, Bergamino M, Polavaram S, Armañanzas R, Ascoli GA, Parekh R. Doubling up on the fly: NeuroMorpho.Org Meets Big Data. Neuroinformatics 2015; 13:127-9. [PMID: 25576225 DOI: 10.1007/s12021-014-9257-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Sumit Nanda
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
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Koelbl C, Helmstaedter M, Lübke J, Feldmeyer D. A barrel-related interneuron in layer 4 of rat somatosensory cortex with a high intrabarrel connectivity. Cereb Cortex 2015; 25:713-25. [PMID: 24076498 PMCID: PMC4318534 DOI: 10.1093/cercor/bht263] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synaptic connections between identified fast-spiking (FS), parvalbumin (PV)-positive interneurons, and excitatory spiny neurons in layer 4 (L4) of the barrel cortex were investigated using patch-clamp recordings and simultaneous biocytin fillings. Three distinct clusters of FS L4 interneurons were identified based on their axonal morphology relative to the barrel column suggesting that these neurons do not constitute a homogeneous interneuron population. One L4 FS interneuron type had an axonal domain strictly confined to a L4 barrel and was therefore named "barrel-confined inhibitory interneuron" (BIn). BIns established reliable inhibitory synaptic connections with L4 spiny neurons at a high connectivity rate of 67%, of which 69% were reciprocal. Unitary IPSPs at these connections had a mean amplitude of 0.9 ± 0.8 mV with little amplitude variation and weak short-term synaptic depression. We found on average 3.7 ± 1.3 putative inhibitory synaptic contacts that were not restricted to perisomatic areas. In conclusion, we characterized a novel type of barrel cortex interneuron in the major thalamo-recipient layer 4 forming dense synaptic networks with L4 spiny neurons. These networks constitute an efficient and powerful inhibitory feedback system, which may serve to rapidly reset the barrel microcircuitry following sensory activation.
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Affiliation(s)
- Christian Koelbl
- Department of Cell Physiology, Max Planck Institute of Medical Research, Jahnstr. 20, D-69120 Heidelberg, Germany
- Current address: Section of Cardiovascular Medicine, Boston University Medical Center, 88 East Newton Street, Boston, MA 02118, USA
| | - Moritz Helmstaedter
- Department of Cell Physiology, Max Planck Institute of Medical Research, Jahnstr. 20, D-69120 Heidelberg, Germany
- Current address: Structure of Neocortical Circuits Group, Max Planck Institute of Neurobiology, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Joachim Lübke
- Institute for Neuroscience and Medicine, INM-2, Research Centre Jülich, Leo-Brandt-Str., D-52425 Jülich, Germany
- Department of Psychiatry, Psychotherapy and Psychosomatics, RWTH Aachen University, Pauwelstr. 30, D-52074 Aachen, Germany
- Jülich-Aachen Research Alliance, Translational Brain Medicine (JARA-Brain), D-52074, Aachen, Germany
| | - Dirk Feldmeyer
- Institute for Neuroscience and Medicine, INM-2, Research Centre Jülich, Leo-Brandt-Str., D-52425 Jülich, Germany
- Department of Psychiatry, Psychotherapy and Psychosomatics, RWTH Aachen University, Pauwelstr. 30, D-52074 Aachen, Germany
- Jülich-Aachen Research Alliance, Translational Brain Medicine (JARA-Brain), D-52074, Aachen, Germany
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9
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Liu C, Yang Y, Hu X, Li JM, Zhang XM, Cai Y, Li Z, Yan XX. Ontogenesis of NADPH-diaphorase positive neurons in guinea pig neocortex. Front Neuroanat 2015; 9:11. [PMID: 25762900 PMCID: PMC4329812 DOI: 10.3389/fnana.2015.00011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/23/2015] [Indexed: 01/29/2023] Open
Abstract
In mammalian cerebrum there exist two distinct types of interneurons expressing nitric oxide synthase (NOS). Type I neurons are large in size and exhibit heavy nicotinamide adenine dinucleotide phosphate diaphorase (NADPH-d) histochemical reaction, while type II cells are small with light NADPH-d reactivity. The time of origin of these cortical neurons relative to corticogenesis remains largely unclear among mammals. Here we explored this issue in guinea pigs using cell birth-dating and double-labeling methods. Bromodeoxyuridine (BrdU) pulse-chasing (2 doses at 50 mg/kg, 12 h apart) was given to time-pregnant mothers, followed by quantification of NADPH-d/BrdU colocalization in the parietal and temporal neocortex in offspring at postnatal day 0 (P0), P30 and P60. Type I neurons were partially colabeled with BrdU at P0, P30 and P60 following pulse-chasing at embryonic day 21 (E21), E28 and E35, varied from 2–11.3% of total population of these neurons for the three time groups. Type II neurons were partially colabeled for BrdU following pulse-chasing at E21, E28, E35 and E42 at P0 (8.6%–16.5% of total population for individual time groups). At P60, type II neurons were found to co-express BrdU (4.8–11.3% of total population for individual time groups) following pulse-chasing at E21, E28, E35, E42, E49, E56 and E60/61. These results indicate that in guinea pigs type I neurons are generated during early corticogenesis, whereas type II cells are produced over a wide prenatal time window persisting until birth. The data also suggest that type II nitrinergic neurons may undergo a period of development/differentiation, for over 1 month, before being NADPH-d reactive.
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Affiliation(s)
- Chao Liu
- Department of Anatomy and Neurobiology, Central South University School of Basic Medical Science Changsha, China ; Department of Neurology, The First Hospital of Changsha Changsha, China
| | - Yan Yang
- Department of Anatomy and Neurobiology, Central South University School of Basic Medical Science Changsha, China ; School of Nursing, Xiangtan Vocational and Technical College Xiangtan, China
| | - Xia Hu
- Department of Anatomy and Neurobiology, Central South University School of Basic Medical Science Changsha, China
| | - Jian-Ming Li
- Department of Anatomy and Neurobiology, Central South University School of Basic Medical Science Changsha, China
| | - Xue-Mei Zhang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University Harbin, China
| | - Yan Cai
- Department of Anatomy and Neurobiology, Central South University School of Basic Medical Science Changsha, China
| | - Zhiyuan Li
- Department of Anatomy and Neurobiology, Central South University School of Basic Medical Science Changsha, China
| | - Xiao-Xin Yan
- Department of Anatomy and Neurobiology, Central South University School of Basic Medical Science Changsha, China
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Dias IA, Bahia CP, Franca JG, Houzel JC, Lent R, Mayer AO, Santiago LF, Silveira LCL, Picanço-Diniz CW, Pereira A. Topography and architecture of visual and somatosensory areas of the agouti. J Comp Neurol 2015; 522:2576-93. [PMID: 24477926 DOI: 10.1002/cne.23550] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 01/17/2014] [Accepted: 01/21/2014] [Indexed: 12/20/2022]
Abstract
We analyzed the organization of the somatosensory and visual cortices of the agouti, a diurnal rodent with a relatively big brain, using a combination of multiunit microelectrode recordings and histological techniques including myelin and cytochrome oxidase staining. We found multiple representations of the sensory periphery in the parietal, temporal, and occipital lobes. While the agouti's primary (V1) and secondary visual areas seemed to lack any obvious modular arrangement, such as blobs or stripes, which are found in some primates and carnivores, the primary somatosensory area (S1) was internally subdivided in discrete regions, isomorphically associated with peripheral structures. Our results confirm and extend previous reports on this species, and provide additional data to understand how variations in lifestyle can influence brain organization in rodents.
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Affiliation(s)
- I A Dias
- Laboratory of Neuroplasticity, Institute of Health Sciences, Universidade Federal do Pará, 66075-110, Belém, (PA), Brazil
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Freire MAM, Santos JR. Distinct morphological features of NADPH diaphorase neurons across rodent's primary cortices. Front Neural Circuits 2013; 7:83. [PMID: 23637654 PMCID: PMC3636462 DOI: 10.3389/fncir.2013.00083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/12/2013] [Indexed: 11/13/2022] Open
Affiliation(s)
- Marco A M Freire
- Laboratory of Cellular Neurobiology, Edmond and Lily Safra International Institute for Neuroscience of Natal Natal, Brazil
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