Faculty Opinions recommendation of Large identified pyramidal cells in macaque motor and premotor cortex exhibit "thin spikes": implications for cell type classification.

2011 ◽  
Author(s):  
Kevan A Martin ◽  
Nuno Miguel MaÇarico Amorim da Costa
Keyword(s):  
Premotor Cortex ◽  
Pyramidal Cells ◽  
Cell Type ◽  
Type Classification

scholarly journals CellO: Comprehensive and hierarchical cell type classification of human cells with the Cell Ontology

2019 ◽  
Author(s):  
Matthew N. Bernstein ◽  
Zhongjie Ma ◽  
Michael Gleicher ◽  
Colin N. Dewey
Keyword(s):  
Single Cell ◽  
Web Application ◽  
Cell Types ◽  
Rna Seq ◽  
Cell Type ◽  
Training Set ◽  
Sequence Read Archive ◽  
Cell Ontology ◽  
Cell Type Specific ◽  
Type Classification

SummaryCell type annotation is a fundamental task in the analysis of single-cell RNA-sequencing data. In this work, we present CellO, a machine learning-based tool for annotating human RNA-seq data with the Cell Ontology. CellO enables accurate and standardized cell type classification by considering the rich hierarchical structure of known cell types, a source of prior knowledge that is not utilized by existing methods. Furthemore, CellO comes pre-trained on a novel, comprehensive dataset of human, healthy, untreated primary samples in the Sequence Read Archive, which to the best of our knowledge, is the most diverse curated collection of primary cell data to date. CellO’s comprehensive training set enables it to run out-of-the-box on diverse cell types and achieves superior or competitive performance when compared to existing state-of-the-art methods. Lastly, CellO’s linear models are easily interpreted, thereby enabling exploration of cell type-specific expression signatures across the ontology. To this end, we also present the CellO Viewer: a web application for exploring CellO’s models across the ontology.HighlightWe present CellO, a tool for hierarchically classifying cell type from single-cell RNA-seq data against the graph-structured Cell OntologyCellO is pre-trained on a comprehensive dataset comprising nearly all bulk RNA-seq primary cell samples in the Sequence Read ArchiveCellO achieves superior or comparable performance with existing methods while featuring a more comprehensive pre-packaged training setCellO is built with easily interpretable models which we expose through a novel web application, the CellO Viewer, for exploring cell type-specific signatures across the Cell OntologyGraphical Abstract

scholarly journals Cell type-specific effects of isoflurane on two distinct afferent inputs to cortical layer 1

2020 ◽  
Author(s):  
Caitlin A. Murphy ◽  
Matthew I. Banks
Keyword(s):  
Ex Vivo ◽  
Brain Slices ◽  
Pyramidal Cells ◽  
Cellular Level ◽  
Cortical Layer ◽  
Cell Type ◽  
Specific Effects ◽  
Primary Mouse ◽  
Cell Type Specific ◽  
Synaptic Responses

ABSTRACTBackgroundWhile their behavioral effects are well-characterized, the mechanisms by which anaesthetics induce loss of consciousness are largely unknown. Anaesthetics may disrupt integration and propagation of information in corticothalamic networks. Recent studies have shown that isoflurane diminishes synaptic responses of thalamocortical (TC) and corticocortical (CC) afferents in a pathway-specific manner. However, whether the synaptic effects of isoflurane observed in extracellular recordings persist at the cellular level has yet to be explored.MethodsHere, we activate TC and CC layer 1 inputs in non-primary mouse neocortex in ex vivo brain slices and explore the degree to which isoflurane modulates synaptic responses in pyramidal cells and in two inhibitory cell populations, somatostatin-positive (SOM+) and parvalbumin-positive (PV+) interneurons.ResultsWe show that the effects of isoflurane on synaptic responses and intrinsic properties of these cells varies among cell type and by cortical layer. Layer 1 inputs to L4 pyramidal cells were suppressed by isoflurane at both TC and CC synapses, while those to L2/3 pyramidal cells and PV+ interneurons were not. TC inputs to SOM+ cells were rarely observed at all, while CC inputs to SOM+ interneurons were robustly suppressed by isoflurane.ConclusionsThese results suggest a mechanism by which isoflurane disrupts integration and propagation of thalamocortical and intracortical signals.

scholarly journals Cell-type specific innervation of cortical pyramidal cells at their apical dendrites

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Ali Karimi ◽  
Jan Odenthal ◽  
Florian Drawitsch ◽  
Kevin M Boergens ◽  
Moritz Helmstaedter
Keyword(s):  
Electron Microscopy ◽  
Pyramidal Cells ◽  
Inhibitory Input ◽  
Cell Type ◽  
Cell Type Specific ◽  
Cortical Regions ◽  
Apical Dendrites ◽  
Computational Properties

We investigated the synaptic innervation of apical dendrites of cortical pyramidal cells in a region between layers (L) 1 and 2 using 3-D electron microscopy applied to four cortical regions in mouse. We found the relative inhibitory input at the apical dendrite’s main bifurcation to be more than 2-fold larger for L2 than L3 and L5 thick-tufted pyramidal cells. Towards the distal tuft dendrites in upper L1, the relative inhibitory input was at least about 2-fold larger for L5 pyramidal cells than for all others. Only L3 pyramidal cells showed homogeneous inhibitory input fraction. The inhibitory-to-excitatory synaptic ratio is thus specific for the types of pyramidal cells. Inhibitory axons preferentially innervated either L2 or L3/5 apical dendrites, but not both. These findings describe connectomic principles for the control of pyramidal cells at their apical dendrites and support differential computational properties of L2, L3 and subtypes of L5 pyramidal cells in cortex.

scholarly journals CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology

iScience ◽  
2021 ◽  
Vol 24 (1) ◽  
pp. 101913
Author(s):  
Matthew N. Bernstein ◽  
Zhongjie Ma ◽  
Michael Gleicher ◽  
Colin N. Dewey
Keyword(s):  
Human Cells ◽  
Cell Type ◽  
Cell Ontology ◽  
Type Classification

Cell-Specific Alterations in Synaptic Properties of Hippocampal CA1 Interneurons After Kainate Treatment

1998 ◽  
Vol 80 (6) ◽  
pp. 2836-2847 ◽  
Author(s):  
F. Morin ◽  
C. Beaulieu ◽  
J.-C. Lacaille
Keyword(s):  
Time Constant ◽  
Decay Time ◽  
Pyramidal Cells ◽  
Stratum Radiatum ◽  
Inhibitory Interneurons ◽  
Cell Type ◽  
Postsynaptic Currents ◽  
Ca1 Region ◽  
Hippocampal Ca1 ◽  
Stratum Lacunosum Moleculare

Morin, F., C. Beaulieu, and J.-C. Lacaille. Cell-specific alterations in synaptic properties of hippocampal CA1 interneurons after kainate treatment. J. Neurophysiol. 80: 2836–2847, 1998. Hippocampal sclerosis and hyperexcitability are neuropathological features of human temporal lobe epilepsy that are reproduced in the kainic acid (KA) model of epilepsy in rats. To assess directly the role of inhibitory interneurons in the KA model, the membrane and synaptic properties of interneurons located in 1) stratum oriens near the alveus (O/A) and 2) at the border of stratum radiatum and stratum lacunosum-moleculare (LM), as well as those of pyramidal cells, were examined with whole cell recordings in slices of control and KA-lesioned rats. In current-clamp recordings, intrinsic cell properties such as action potential amplitude and duration, amplitude of fast and medium duration afterhyperpolarizations, membrane time constant, and input resistance were generally unchanged in all cell types after KA treatment. In voltage-clamp recordings, the amplitude and conductance of pharmacologically isolated excitatory postsynaptic currents (EPSCs) were significantly reduced in LM interneurons of KA-treated animals but were not significantly changed in O/A and pyramidal cells. The rise time of EPSCs was not significantly changed in any cell type after KA treatment. In contrast, the decay time constant of EPSCs was significantly faster in O/A interneurons of KA-treated rats but was unchanged in LM and pyramidal cells. The amplitude and conductance of pharmacologically isolated γ-aminobutyric acid-A (GABAA) inhibitory postsynaptic currents (IPSCs) were not significantly changed in any cell type of KA-treated rats. The rise time and decay time constant of GABAA IPSCs were significantly faster in pyramidal cells of KA-treated rats but were not significantly changed in O/A and LM interneurons. These results suggest that complex alterations in synaptic currents occur in specific subpopulations of inhibitory interneurons in the CA1 region after KA lesions. A reduction of evoked excitatory drive onto inhibitory cells located at the border of stratum radiatum and stratum lacunosum-moleculare may contribute to disinhibition and polysynaptic epileptiform activity in the CA1 region. Compensatory changes, involving excitatory synaptic transmission on other interneuron subtypes and inhibitory synaptic transmission on pyramidal cells, may also take place and contribute to the residual, functional monosynaptic inhibition observed in principal cells after KA treatment.

scholarly journals Characterization of Single-Nucleus Electrical Properties by Microfluidic Constriction Channel

Micromachines ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 740 ◽  
Author(s):  
Hongyan Liang ◽  
Yi Zhang ◽  
Deyong Chen ◽  
Huiwen Tan ◽  
Yu Zheng ◽  
...  
Keyword(s):  
Unit Area ◽  
Electrical Characterization ◽  
Electrical Model ◽  
Cell Type ◽  
Whole Cells ◽  
Single Nucleus ◽  
Nuclear Isolation ◽  
New Perspective ◽  
Type Classification

As key bioelectrical markers, equivalent capacitance (Cne, i.e., capacitance per unit area) and resistance (Rne, i.e., resistivity multiply thickness) of nuclear envelopes have emerged as promising electrical indicators, which cannot be effectively measured by conventional approaches. In this study, single nuclei were isolated from whole cells and trapped at the entrances of microfluidic constriction channels, and then corresponding impedance profiles were sampled and translated into single-nucleus Cne and Rne based on a home-developed equivalent electrical model. Cne and Rne of A549 nuclei were first quantified as 3.43 ± 1.81 μF/cm2 and 2.03 ± 1.40 Ω·cm2 (Nn = 35), which were shown not to be affected by variations of key parameters in nuclear isolation and measurement. The developed approach in this study was also used to measure a second type of nuclei, producing Cne and Rne of 3.75 ± 3.17 μF/cm2 and 1.01 ± 0.70 Ω·cm2 for SW620 (Nn = 17). This study may provide a new perspective in single-cell electrical characterization, enabling cell type classification and cell status evaluation based on bioelectrical markers of nuclei.

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