scholarly journals ShuTu: Open-Source Software for Efficient and Accurate Reconstruction of Dendritic Morphology

2017 ◽  
Author(s):  
Dezhe Z. Jin ◽  
Ting Zhao ◽  
David L. Hunt ◽  
Rachel P. Tillage ◽  
Ching-Lung Hsu ◽  
...  
Keyword(s):  
Software Package ◽  
Three Dimensional ◽  
Dendritic Structure ◽  
Dendritic Tree ◽  
Structural Data ◽  
Computer Models ◽  
Dendritic Morphology ◽  
Automated Identification ◽  
Action Potential Firing ◽  
Potential Firing

AbstractNeurons perform computations by integrating inputs from thousands of synapses – mostly in the dendritic tree – to drive action potential firing in the axon. One fruitful approach to understanding this process is to record from neurons using patch-clamp electrodes, fill the recorded neuron with a substance that allows subsequent staining, reconstruct the three-dimensional architecture of the dendrites, and use the resulting functional and structural data to develop computer models of dendritic integration. Accurately producing quantitative reconstructions of dendrites is typically a tedious process taking many hours of manual inspection and measurement. Here we present ShuTu, a new software package that facilitates accurate and efficient reconstruction of dendrites imaged using bright-field microscopy. The program operates in two steps: (1) automated identification of dendritic process, and (2) manual correction of errors in the automated reconstruction. This approach allows neurons with complex dendritic morphologies to be reconstructed rapidly and efficiently, thus facilitating the use of computer models to study dendritic structure-function relationships and the computations performed by single neurons.Significance StatementWe developed a software package – ShuTu – that integrates automated reconstruction of stained neurons with manual error correction. This package facilitates rapid reconstruction of the three-dimensional geometry of neuronal dendritic trees, often needed for computational simulations of the functional properties of these structures.

scholarly journals Distance-dependent regulation of NMDAR nanoscale organization along hippocampal neuron dendrites

2020 ◽  
Vol 117 (39) ◽  
pp. 24526-24533
Author(s):  
Joana S. Ferreira ◽  
Julien P. Dupuis ◽  
Blanka Kellermayer ◽  
Nathan Bénac ◽  
Constance Manso ◽  
...  
Keyword(s):  
Hippocampal Neurons ◽  
Pyramidal Neurons ◽  
Dendritic Tree ◽  
Synaptic Proteins ◽  
Glutamatergic Synapses ◽  
Action Potential Firing ◽  
Hippocampal Pyramidal Neurons ◽  
Calcium Calmodulin Dependent ◽  
Potential Firing ◽  
Nanoscale Topography

Hippocampal pyramidal neurons are characterized by a unique arborization subdivided in segregated dendritic domains receiving distinct excitatory synaptic inputs with specific properties and plasticity rules that shape their respective contributions to synaptic integration and action potential firing. Although the basal regulation and plastic range of proximal and distal synapses are known to be different, the composition and nanoscale organization of key synaptic proteins at these inputs remains largely elusive. Here we used superresolution imaging and single nanoparticle tracking in rat hippocampal neurons to unveil the nanoscale topography of native GluN2A- and GluN2B-NMDA receptors (NMDARs)—which play key roles in the use-dependent adaptation of glutamatergic synapses—along the dendritic arbor. We report significant changes in the nanoscale organization of GluN2B-NMDARs between proximal and distal dendritic segments, whereas the topography of GluN2A-NMDARs remains similar along the dendritic tree. Remarkably, the nanoscale organization of GluN2B-NMDARs at proximal segments depends on their interaction with calcium/calmodulin-dependent protein kinase II (CaMKII), which is not the case at distal segments. Collectively, our data reveal that the nanoscale organization of NMDARs changes along dendritic segments in a subtype-specific manner and is shaped by the interplay with CaMKII at proximal dendritic segments, shedding light on our understanding of the functional diversity of hippocampal glutamatergic synapses.

scholarly journals Sensory experience controls dendritic structure and behavior by distinct pathways involving degenerins

2018 ◽  
Author(s):  
Sharon Inberg ◽  
Benjamin Podbilewicz
Keyword(s):  
Behavioral Plasticity ◽  
Dendritic Structure ◽  
Dendritic Tree ◽  
Structure And Function ◽  
Dendritic Morphology ◽  
Epithelial Sodium Channels ◽  
And Function ◽  
And Behavior ◽  
Activity Dependent ◽  
Stimulation Of

AbstractTree-like neurites are crucial for receiving information into neurons. It is assumed that nurturing affects the structure and function of dendrites, yet the evidence is scarce, and the mechanisms are unknown. To study whether mechanosensory experience affects dendritic morphology, we use natural mechanical stimulation of the Caenorhabditis elegans’ polymodal PVD neurons, induced by physical contacts between individuals. We found that animal isolation affects the dendritic tree structure of the PVD. Moreover, developmentally isolated animals show a decrease in their ability to respond to harsh touch. The structural and behavioral plasticity following mechanosensory deprivation are functionally independent of each other and are mediated by an array of evolutionary conserved amiloride-sensitive epithelial sodium channels (degenerins). Our results suggest an activity-dependent homeostatic mechanism for dendritic structural plasticity, acting downstream to mechanosensory activation of degenerins.

Simulating Self-Regeneration and Self-Replication Processes Using Movable Cellular Automata with a Mutual Equilibrium Neighborhood

2020 ◽  
Vol 29 (4) ◽  
pp. 741-757
Author(s):  
Kateryna Hazdiuk ◽  
◽  
Volodymyr Zhikharevich ◽  
Serhiy Ostapov ◽  
◽  
...  
Keyword(s):  
Cellular Automata ◽  
Cellular Automaton ◽  
Three Dimensional ◽  
Computer Models ◽  
The Self ◽  
Model Construction ◽  
Natural Phenomena ◽  
Different Types ◽  
Movable Cellular Automata ◽  
Self Replication

This paper deals with the issue of model construction of the self-regeneration and self-replication processes using movable cellular automata (MCAs). The rules of cellular automaton (CA) interactions are found according to the concept of equilibrium neighborhood. The method is implemented by establishing these rules between different types of cellular automata (CAs). Several models for two- and three-dimensional cases are described, which depict both stable and unstable structures. As a result, computer models imitating such natural phenomena as self-replication and self-regeneration are obtained and graphically presented.

scholarly journals Three-Dimensional Structures of Carbohydrates and Where to Find Them

2020 ◽  
Vol 21 (20) ◽  
pp. 7702 ◽  
Author(s):  
Sofya I. Scherbinina ◽  
Philip V. Toukach
Keyword(s):  
Experimental Data ◽  
Molecular Modeling ◽  
Computational Methods ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Data ◽  
Structural Features ◽  
Data Validation ◽  
Data Generation ◽  
Efficient Treatment

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

scholarly journals Zinc Enhances the Inhibitory Effects of Strychnine-Sensitive Glycine Receptors in Mouse Hippocampal Neurons

2007 ◽  
Vol 98 (6) ◽  
pp. 3666-3676 ◽  
Author(s):  
Hai Xia Zhang ◽  
Liu Lin Thio
Keyword(s):  
Action Potential ◽  
Action Potentials ◽  
Hippocampal Neurons ◽  
Neuronal Excitability ◽  
Hippocampal Slices ◽  
Glycine Receptors ◽  
Inhibitory Effects ◽  
Action Potential Firing ◽  
Embryonic Mouse ◽  
Potential Firing

Although extracellular Zn2+ is an endogenous biphasic modulator of strychnine-sensitive glycine receptors (GlyRs), the physiological significance of this modulation remains poorly understood. Zn2+ modulation of GlyR may be especially important in the hippocampus where presynaptic Zn2+ is abundant. Using cultured embryonic mouse hippocampal neurons, we examined whether 1 μM Zn2+, a potentiating concentration, enhances the inhibitory effects of GlyRs activated by sustained glycine applications. Sustained 20 μM glycine (EC25) applications alone did not decrease the number of action potentials evoked by depolarizing steps, but they did in 1 μM Zn2+. At least part of this effect resulted from Zn2+ enhancing the GlyR-induced decrease in input resistance. Sustained 20 μM glycine applications alone did not alter neuronal bursting, a form of hyperexcitability induced by omitting extracellular Mg2+. However, sustained 20 μM glycine applications depressed neuronal bursting in 1 μM Zn2+. Zn2+ did not enhance the inhibitory effects of sustained 60 μM glycine (EC70) applications in these paradigms. These results suggest that tonic GlyR activation could decrease neuronal excitability. To test this possibility, we examined the effect of the GlyR antagonist strychnine and the Zn2+ chelator tricine on action potential firing by CA1 pyramidal neurons in mouse hippocampal slices. Co-applying strychnine and tricine slightly but significantly increased the number of action potentials fired during a depolarizing current step and decreased the rheobase for action potential firing. Thus Zn2+ may modulate neuronal excitability normally and in pathological conditions such as seizures by potentiating GlyRs tonically activated by low agonist concentrations.

scholarly journals The Application of Visual Environmental Economics in the Study of Public Preference and Urban Greenspace

2009 ◽  
Vol 36 (2) ◽  
pp. 355-375 ◽  
Author(s):  
Richard Laing ◽  
Anne-Marie Davies ◽  
David Miller ◽  
Anna Conniff ◽  
Stephen Scott ◽  
...  
Keyword(s):  
Environmental Economic ◽  
Environmental Economics ◽  
Environmental Conditions ◽  
Three Dimensional ◽  
Computer Models ◽  
Time Of Day ◽  
Public Preference ◽  
Daily Lives ◽  
Urban Greenspace ◽  
Physical Variables

Urban greenspace has consistently been argued to be of great importance to the wellbeing, health, and daily lives of residents and users. This paper reports results from a study that combined the visualisation of public results from a study that combined the visualisation of public greenspace with environmental economics, and that aimed to develop a method by which realistic computer models of sites could be used within preference studies. As part of a methodology that employed contingent rating to establish the values placed on specific greenspace sites, three-dimensional computer models were used to produce visualisations of particular environmental conditions. Of particular importance to the study was the influence of variables including lighting, season, time of day, and weather on the perception of respondents. This study followed previous work that established a suitable approach to the modelling and testing of entirely moveable physical variables within the built environment. As such, the study has established firmly that computer-generated visualisations are appropriate for use within environmental economic surveys, and that there is potential for a holistic range of attributes to be included in such studies.

scholarly journals The thalamic low-threshold Ca 2+ potential: a key determinant of the local and global dynamics of the slow (<1 Hz) sleep oscillation in thalamocortical networks

2011 ◽  
Vol 369 (1952) ◽  
pp. 3820-3839 ◽  
Author(s):  
Vincenzo Crunelli ◽  
Adam C. Errington ◽  
Stuart W. Hughes ◽  
Tibor I. Tóth
Keyword(s):  
Action Potential ◽  
Slow Oscillation ◽  
Global Dynamics ◽  
Action Potential Firing ◽  
Local And Global Dynamics ◽  
Up States ◽  
Potential Firing ◽  
Low Threshold

During non-rapid eye movement sleep and certain types of anaesthesia, neurons in the neocortex and thalamus exhibit a distinctive slow (<1 Hz) oscillation that consists of alternating UP and DOWN membrane potential states and which correlates with a pronounced slow (<1 Hz) rhythm in the electroencephalogram. While several studies have claimed that the slow oscillation is generated exclusively in neocortical networks and then transmitted to other brain areas, substantial evidence exists to suggest that the full expression of the slow oscillation in an intact thalamocortical (TC) network requires the balanced interaction of oscillator systems in both the neocortex and thalamus. Within such a scenario, we have previously argued that the powerful low-threshold Ca 2+ potential (LTCP)-mediated burst of action potentials that initiates the UP states in individual TC neurons may be a vital signal for instigating UP states in related cortical areas. To investigate these issues we constructed a computational model of the TC network which encompasses the important known aspects of the slow oscillation that have been garnered from earlier in vivo and in vitro experiments. Using this model we confirm that the overall expression of the slow oscillation is intricately reliant on intact connections between the thalamus and the cortex. In particular, we demonstrate that UP state-related LTCP-mediated bursts in TC neurons are proficient in triggering synchronous UP states in cortical networks, thereby bringing about a synchronous slow oscillation in the whole network. The importance of LTCP-mediated action potential bursts in the slow oscillation is also underlined by the observation that their associated dendritic Ca 2+ signals are the only ones that inform corticothalamic synapses of the TC neuron output, since they, but not those elicited by tonic action potential firing, reach the distal dendritic sites where these synapses are located.

BICUCULLINE/BACLOFEN-INSENSITIVE GABA RESPONSE IN CRUSTACEAN NEURONES IN CULTURE

1994 ◽  
Vol 191 (1) ◽  
pp. 167-193
Author(s):  
C Jackel ◽  
W Krenz ◽  
F Nagy
Keyword(s):  
Reversal Potential ◽  
Membrane Conductance ◽  
Gamma Aminobutyric Acid ◽  
Action Potential Firing ◽  
Patch Clamp Technique ◽  
Conformationally Restricted ◽  
Whole Cell Patch Clamp ◽  
Gabac Receptor ◽  
Potential Firing ◽  
Sr 95531

Neurones were dissociated from thoracic ganglia of embryonic and adult lobsters and kept in primary culture. When gamma-aminobutyric acid (GABA) was applied by pressure ejection, depolarizing or hyperpolarizing responses were produced, depending on the membrane potential. They were accompanied by an increase in membrane conductance. When they were present, action potential firing was inhibited. The pharmacological profile and ionic mechanism of GABA-evoked current were investigated under voltage-clamp with the whole-cell patch-clamp technique. The reversal potential of GABA-evoked current depended on the intracellular and extracellular Cl- concentration but not on extracellular Na+ and K+. Blockade of Ca2+ channels by Mn2+ was also without effect. The GABA-evoked current was mimicked by application of the GABAA agonists muscimol and isoguvacine with an order of potency muscimol&gt;GABA&gt;isoguvacine. cis-4-aminocrotonic acid (CACA), a folded and conformationally restricted GABA analogue, supposed to be diagnostic for the vertebrate GABAC receptor, also induced a bicuculline-resistant chloride current, although with a potency about 10 times lower than that of GABA. The GABA-evoked current was largely blocked by picrotoxin, but was insensitive to the GABAA antagonists bicuculline, bicuculline methiodide and SR 95531 at concentrations of up to 100 &micro;mol l-1. Diazepam and phenobarbital did not exert modulatory effects. The GABAB antagonist phaclophen did not affect the GABA-induced current, while the GABAB agonists baclophen and 3-aminopropylphosphonic acid (3-APA) never evoked any response. Our results suggest that lobster thoracic neurones in culture express a chloride-conducting GABA-receptor channel which conforms to neither the GABAA nor the GABAB types of vertebrates but shows a pharmacology close to that of the novel GABAC receptor described in the vertebrate retina.

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