scholarly journals A connectomic study of a petascale fragment of human cerebral cortex

2021 ◽  
Author(s):  
Alexander Shapson-Coe ◽  
Michal Januszewski ◽  
Daniel R Berger ◽  
Art Pope ◽  
Yuelong Wu ◽  
...  
Keyword(s):  
Cerebral Cortex ◽  
High Speed ◽  
Pyramidal Neurons ◽  
Three Dimensional ◽  
Cell Types ◽  
Dimensional Structure ◽  
Inhibitory Synapses ◽  
Excitatory Synapses ◽  
Split And Merge ◽  
Surgical Sample

We acquired a rapidly preserved human surgical sample from the temporal lobe of the cerebral cortex. We stained a 1 mm3 volume with heavy metals, embedded it in resin, cut more than 5000 slices at ~30 nm and imaged these sections using a high-speed multibeam scanning electron microscope. We used computational methods to render the three-dimensional structure of 50,000 cells, hundreds of millions of neurites and 130 million synaptic connections. The 1.3 petabyte electron microscopy volume, the segmented cells, cell parts, blood vessels, myelin, inhibitory and excitatory synapses, and 100 manually proofread cells are available to peruse online. Despite the incompleteness of the automated segmentation caused by split and merge errors, many interesting features were evident. Glia outnumbered neurons 2:1 and oligodendrocytes were the most common cell type in the volume. The E:I balance of neurons was 69:31%, as was the ratio of excitatory versus inhibitory synapses in the volume. The E:I ratio of synapses was significantly higher on pyramidal neurons than inhibitory interneurons. We found that deep layer excitatory cell types can be classified into subsets based on structural and connectivity differences, that chandelier interneurons not only innervate excitatory neuron initial segments as previously described, but also each others initial segments, and that among the thousands of weak connections established on each neuron, there exist rarer highly powerful axonal inputs that establish multi-synaptic contacts (up to ~20 synapses) with target neurons. Our analysis indicates that these strong inputs are specific, and allow small numbers of axons to have an outsized role in the activity of some of their postsynaptic partners.

Three-dimensional structure of dendritic spines, neuronal specializations that impart both stability and flexibility to synaptic function

1993 ◽  
Vol 51 ◽  
pp. 92-93
Author(s):  
Kristen M. Harris
Keyword(s):  
Dendritic Spines ◽  
Three Dimensional ◽  
Synaptic Function ◽  
Dimensional Structure ◽  
Excitatory Synapses ◽  
Concept Of Function ◽  
Section Electron ◽  
High Quality Information ◽  
The Central Nervous System ◽  
Mathematical Analyses

Dendritic spines are the tiny protrusions that stud the surface of many neurons and they are the location of over 90% of all excitatory synapses that occur in the central nervous system. Their small size and variable shapes has in large part made detailed study of their structure refractory to conventional light microscopy and single section electron microscopy (EM). Yet their widespread occurrence and likely involvement in learning and memory has motivated extensive efforts to obtain quantitative descriptions of spines in both steady state and dynamic conditions. Since the seminal mathematical analyses of D’Arcy Thompson, the power of establishing quantitatively key parameters of structure has become recognized as a foundation of successful biological inquiry. For dendritic spines highly precise determinations of structure and its variation are proving themselves as the kingpin for establishing a valid concept of function. The recent conjunction of high quality information about the structure, function, and theoretical implications of dendritic spines has produced a flurry of new considerations of their role in synaptic transmission.

scholarly journals Integration, coincidence detection and resonance in networks of spiking neurons expressing Gamma oscillations and asynchronous states

2021 ◽  
Vol 17 (9) ◽  
pp. e1009416
Author(s):  
Eduarda Susin ◽  
Alain Destexhe
Keyword(s):  
Cerebral Cortex ◽  
Pyramidal Neurons ◽  
Network Models ◽  
Cell Types ◽  
Gamma Oscillations ◽  
Coincidence Detection ◽  
Biophysical Models ◽  
Firing Mode ◽  
Different Cell Types ◽  
External Stimuli

Gamma oscillations are widely seen in the awake and sleeping cerebral cortex, but the exact role of these oscillations is still debated. Here, we used biophysical models to examine how Gamma oscillations may participate to the processing of afferent stimuli. We constructed conductance-based network models of Gamma oscillations, based on different cell types found in cerebral cortex. The models were adjusted to extracellular unit recordings in humans, where Gamma oscillations always coexist with the asynchronous firing mode. We considered three different mechanisms to generate Gamma, first a mechanism based on the interaction between pyramidal neurons and interneurons (PING), second a mechanism in which Gamma is generated by interneuron networks (ING) and third, a mechanism which relies on Gamma oscillations generated by pacemaker chattering neurons (CHING). We find that all three mechanisms generate features consistent with human recordings, but that the ING mechanism is most consistent with the firing rate change inside Gamma bursts seen in the human data. We next evaluated the responsiveness and resonant properties of these networks, contrasting Gamma oscillations with the asynchronous mode. We find that for both slowly-varying stimuli and precisely-timed stimuli, the responsiveness is generally lower during Gamma compared to asynchronous states, while resonant properties are similar around the Gamma band. We could not find conditions where Gamma oscillations were more responsive. We therefore predict that asynchronous states provide the highest responsiveness to external stimuli, while Gamma oscillations tend to overall diminish responsiveness.

scholarly journals High-Speed Volumetric Observation of a Wet Microburst Using X-Band Phased Array Weather Radar in Japan

2016 ◽  
Vol 144 (10) ◽  
pp. 3749-3765 ◽  
Author(s):  
Toru Adachi ◽  
Kenichi Kusunoki ◽  
Satoru Yoshida ◽  
Ken-ichiro Arai ◽  
Tomoo Ushio
Keyword(s):  
High Speed ◽  
Phased Array ◽  
Three Dimensional ◽  
Weather Radar ◽  
Ground Level ◽  
Dimensional Structure ◽  
Convection Cell ◽  
Low Level ◽  
X Band ◽  
Traffic Operation

This paper reports a high-speed volumetric observation of a wet microburst event using X-band phased array weather radar (PAWR) in Japan. On 10 September 2014, PAWR observed the three-dimensional structure of a convection cell, which had a vertical extent of 5–6 km and a horizontal dimension of 2–10 km, moving toward the east-northeast. At 2310 Japan standard time (JST), a precipitation core with a radar reflectivity of >40 dBZ appeared at 3–5 km above ground level. The core then increased in size and intensity and rapidly descended to the ground. During this time, a reflectivity notch associated with midlevel inflow was initially formed near the top of the precipitation core and, subsequently, at lower altitudes. A strong low-level outflow with a radial divergence of >4 × 10−3 s−1 appeared just below the notch at around 2321 JST. The outflow lasted for approximately 13 min and eventually disappeared after 2333 JST along with dissipation of the causative storm cell. These results suggest that, in addition to hydrometeor loading, evaporative cooling due to the entrainment of midlevel relatively dry air played an additional role in driving a strong downdraft. The preceding signatures including descending precipitation core, reflectivity notch, and midlevel convergence observed by PAWR are useful precursors to forecast the occurrence of low-level wind shear 5–10 min ahead, which is important for safe air traffic operation.

Effect of Liquid Properties on Thermal Mixing in a T-Junction

2014 ◽  
Author(s):  
O. N. Kashinsky ◽  
P. D. Lobanov ◽  
A. S. Kurdyumov ◽  
N. A. Pribaturin
Keyword(s):  
Temperature Field ◽  
High Speed ◽  
Three Dimensional ◽  
Infrared Image ◽  
Infrared Camera ◽  
Dimensional Structure ◽  
Thin Wall ◽  
Channel Diameter ◽  
Different Temperatures ◽  
Different Diameters

Results of experimental study of mixing of liquids with different temperatures in a T-junction are presented. Experiments were performed with liquids which have significantly different physical properties. The liquid with higher temperature was injected through the branch of the T-junction. The test section was made of thin wall stainless tubes. The distribution of wall temperature over the surface was measured using a high speed infrared camera. Both time averaged and fluctuational characteristics of the temperature field were obtained from infrared image processing. The structure of temperature field inside the channel was measured by a microthermocouple. It was mounted on the traversing unit which allowed its translation along the channel diameter. Measurements were made over different diameters in the same cross section. This allowed to construct the three-dimensional structure of the temperature field. Results obtained provide experimental data necessary for validation of thermo hydraulic codes for the design of power equipment.

scholarly journals Comparative 2D and 3D Ultrastructural Analyses of Dendritic Spines from CA1 Pyramidal Neurons in the Mouse Hippocampus

2021 ◽  
Vol 22 (3) ◽  
pp. 1188
Author(s):  
Maria Nicol Colombo ◽  
Greta Maiellano ◽  
Sabrina Putignano ◽  
Lucrezia Scandella ◽  
Maura Francolini
Keyword(s):  
Pyramidal Neurons ◽  
Brain Connectivity ◽  
Three Dimensional ◽  
Excitatory Synapses ◽  
Spine Density ◽  
Functional Impairments ◽  
Small Complex ◽  
Hippocampal Ca1 ◽  
3D Em ◽  
2D And 3D

Three-dimensional (3D) reconstruction from electron microscopy (EM) datasets is a widely used tool that has improved our knowledge of synapse ultrastructure and organization in the brain. Rearrangements of synapse structure following maturation and in synaptic plasticity have been broadly described and, in many cases, the defective architecture of the synapse has been associated to functional impairments. It is therefore important, when studying brain connectivity, to map these rearrangements with the highest accuracy possible, considering the affordability of the different EM approaches to provide solid and reliable data about the structure of such a small complex. The aim of this work is to compare quantitative data from two dimensional (2D) and 3D EM of mouse hippocampal CA1 (apical dendrites), to define whether the results from the two approaches are consistent. We examined asymmetric excitatory synapses focusing on post synaptic density and dendritic spine area and volume as well as spine density, and we compared the results obtained with the two methods. The consistency between the 2D and 3D results questions the need—for many applications—of using volumetric datasets (costly and time consuming in terms of both acquisition and analysis), with respect to the more accessible measurements from 2D EM projections.

scholarly journals In situstructures of periplasmic flagella inBorreliareveals conformational changes essential for flagellar rotation

2019 ◽  
Author(s):  
Yunjie Chang ◽  
Kihwan Moon ◽  
Xiaowei Zhao ◽  
J. Norris Steven ◽  
Md A. Motaleb ◽  
...  
Keyword(s):  
Conformational Change ◽  
Conformational Changes ◽  
High Speed ◽  
Electron Tomography ◽  
Proton Translocation ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Flagellar Motor ◽  
Flagellar Filament ◽  
Flagellar Rotation

SUMMARYThe bacterial flagellar motor is a molecular machine that rotates the flagellar filament at high speed. Torque is generated by the stator-rotor interaction coupled to an ion flux through the torque-generating stator. Here, we employed cryo-electron tomography to visualize the intact flagellar motor in the Lyme disease spirocheteBorrelia burgdorferi. By analysis of the motor structures of wild-type and stator mutants, we localize the torque-generating units precisely and determine three-dimensional structure of the stator and its interactions with the rotor. Our study shows that the cytoplasmic domains of the stator are packed regularly around the circumference of the flagellar C-ring. The stator-rotor interaction induces a profound conformational change in the C-ring. Analysis of the motors of a less motilemotB-D24E mutant and a non-motilemotB-D24N mutant, in which the proton translocation is reduced and blocked, respectively, provides evidence that the conformational change of the C-ring is essential for flagellar rotation.

scholarly journals Continued blood cell formation in spherical bodies in a long-term mouse spleen culture

Blood ◽  
1991 ◽  
Vol 77 (6) ◽  
pp. 1211-1217
Author(s):  
Y Matsuya ◽  
N Yanai ◽  
H Ohtani ◽  
H Naganuma ◽  
M Obinata
Keyword(s):  
Blood Cell ◽  
Cell Formation ◽  
Three Dimensional ◽  
Cell Types ◽  
Spherical Body ◽  
The Body ◽  
Dimensional Structure ◽  
Newborn Mice ◽  
Prolonged Culture

During the primary culture of spleen fragments of newborn mice, a spherical body (d = circa 200 to 300 microns) as a three-dimensional cellular organization was formed. Continued production of blood cells from the spherical body was observed without changing its size for about 2 months of culture. Without growth factor, the spherical bodies produced mainly lymphocytes and macrophages. Addition of interleukin-3 enhanced their granulocyte formation, and this enhancement was observed even after a prolonged maintenance without growth factors. The spherical bodies were composed of a uniform mixture of endothelial cells and fibroblasts within the body, and cell-cell contacts between lymphocytes and fibroblasts were notable in the periphery. With prolonged culture, the spherical bodies showed a definite change in their structure by sorting two cell types and the blood cell production gradually decreased. These results suggested that a three-dimensional structure was required for the maintenance, growth, and differentiation of blood cell progenitors in the long-term spleen culture.

scholarly journals Integration, coincidence detection and resonance in networks of spiking neurons expressing gamma oscillations and asynchronous states

2021 ◽  
Author(s):  
Eduarda Susin ◽  
Alain Destexhe
Keyword(s):  
Cerebral Cortex ◽  
Pyramidal Neurons ◽  
Network Models ◽  
Cell Types ◽  
Gamma Oscillations ◽  
Coincidence Detection ◽  
Biophysical Models ◽  
Firing Mode ◽  
Different Cell Types ◽  
External Stimuli

Gamma oscillations are widely seen in the awake and sleeping cerebral cortex, but the exact role of these oscillations is still debated. Here, we used biophysical models to examine how gamma oscillations may participate to the processing of afferent stimuli. We constructed conductance-based network models of gamma oscillations, based on different cell types found in cerebral cortex. The models were adjusted to extracellular unit recordings in humans, where gamma oscillations always coexist with the asynchronous firing mode. We considered three different mechanisms to generate gamma, first a mechanism based on the interaction between pyramidal neurons and interneurons (PING), second a mechanism in which gamma is generated in interneuron networks (ING) and third, a mechanism which relies on gamma oscillations generated by pacemaker Chattering neurons (CHING). We find that all three mechanisms generate features consistent with human recordings, but that the ING mechanism is most consistent with the firing rate change inside Gamma bursts seen in the human data. We next evaluated the responsiveness and resonant properties of these networks, contrasting gamma oscillations with the asynchronous mode. We find that for both slowly-varying stimuli and precisely-timed stimuli, the responsiveness is generally lower during Gamma compared to asynchronous states, while resonant properties are similar around the Gamma band. We could not find conditions where Gamma oscillations were more responsive. We therefore predict that asynchronous states provide the highest responsiveness to external stimuli, while Gamma oscillations tend to overall diminish responsiveness.

Sizes of Particles, Clumps, and Gaps Within the Strong Janus 2:1 and Mimas 5:3 Density Waves from Cassini UVIS Stellar Occultation Data Statistics

2020 ◽  
Author(s):  
Stephanie Eckert ◽  
Joshua Colwell ◽  
Richard Jerousek ◽  
Larry Esposito
Keyword(s):  
High Speed ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Density Waves ◽  
Sight Distance ◽  
Wide Range ◽  
Stellar Occultations ◽  
Occultation Data ◽  
Self Gravity ◽  
Ring Material

<p>The high-speed photometer of Cassini’s Ultraviolet Imaging Spectrograph (UVIS) collected data from stellar occultations across Saturn’s rings at unprecedented high resolution over a wide range of viewing geometries. Because photon counts are described by Poisson statistics, we expect a variance equal to the mean in the absence of intervening ring material. However, most ring ‘particles’ are truly aggregates of smaller particles, ranging from micron-size dust to tens of meter-sized boulders, and if the sizes of these aggregates are not small relative to the field-of-view over a single integration period, they introduce excess variance from which we can glean further information about the sizes of particles and clumps. This is particularly relevant in the A ring, where non-axisymmetric self-gravity wakes are ubiquitous. Larger elongated clumps nicknamed straw have been directly imaged in the troughs of strong density waves (Porco et al., 2005, Science, 307, 1226-1236). In this work we present a survey of the statistical moments of variance and skewness for several ring stellar occultations at two strong density waves from different ring regions, Janus 2:1 and Mimas 5:3, over a variety of viewing angles. The line-of-sight distance from Cassini to the rings affects the measurement area due to the scattered signal and diffraction, and different viewing angles provide measurements of the same ring material with different aspects to potentially reveal the three-dimensional structure of clumps. We calculate an effective particle size per integration area, R, derived by Colwell et al., (2018, Icarus, 300, 150-166) and find similar values for R in both peaks and troughs across density waves as well as within density waves and in adjacent regions. We observe strong statistical similarity between troughs and regions adjoining the waves with overall higher skewness in the A ring, indicating more clumping and greater asymmetry in this region than in the inner B ring region.</p>

BSSB:BLASTServer for Structural Biologists

2011 ◽  
Vol 44 (3) ◽  
pp. 651-654 ◽  
Author(s):  
Muthukumarasamy Uthayakumar ◽  
Govindhan Sowmiya ◽  
Radhakrishnan Sabarinathan ◽  
N. Udayaprakash ◽  
M. Kirti Vaishnavi ◽  
...  
Keyword(s):  
High Speed ◽  
Three Dimensional ◽  
Pairwise Alignment ◽  
Query Protein ◽  
Dimensional Structure ◽  
Local Alignment ◽  
Three Dimensional Structure ◽  
Level Information ◽  
Search Tool ◽  
The Subject

The Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs with which similarity searches, for both protein and nucleic acid sequences, can be performed against large databases at high speed. A large number of tools exist for processingBLASToutput, but none of them provide three-dimensional structure visualization. This shortcoming has been addressed in the proposed toolBLASTServer for Structural Biologists (BSSB), which maps aBLASToutput onto the three-dimensional structure of the subject protein. The three-dimensional structure of the subject protein is represented using a three-color coding scheme (identical: red; similar: yellow; and mismatch: white) based on the pairwise alignment obtained. Thus, the user will be able to visualize a possible three-dimensional structure for the query protein sequence. This information can be used to gain a deeper insight into the sequence–structure correlation. Furthermore, the additional structure-level information enables the user to make coherent and logical decisions regarding the type of input model structure or fragment that can be used for molecular replacement calculations. This tool is freely available to all users at http://bioserver1.physics.iisc.ernet.in/bssb/.

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