scholarly journals Volume-CLEM: a method for correlative light and electron microscopy in three dimensions

2019 ◽  
Vol 317 (6) ◽  
pp. L778-L784 ◽  
Author(s):  
Jan Hegermann ◽  
Christoph Wrede ◽  
Susanne Fassbender ◽  
Ronja Schliep ◽  
Matthias Ochs ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Light And Electron Microscopy ◽  
Three Dimensional ◽  
Fluorescent Labeling ◽  
Three Dimensions ◽  
Data Sets ◽  
New Approach ◽  
3D Data ◽  
Wide Range ◽  
3D Em

Generation of three-dimensional (3D) data sets from serial sections of tissues imaged by light microscopy (LM) allows identification of rare structures by morphology or fluorescent labeling. Here, we demonstrate a workflow for correlative LM and electron microscopy (EM) from 3D LM to 3D EM, using the same sectioned material for both methods consecutively. The new approach is easy to reproduce in routine EM laboratories and applicable to a wide range of organs and research questions.

scholarly journals Imaging Viral Factories

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 3
Author(s):  
Cristina Risco Ortiz
Keyword(s):  
Electron Microscopy ◽  
Viral Replication ◽  
Molecular Mapping ◽  
Light And Electron Microscopy ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Particle Assembly ◽  
Intracellular Compartments ◽  
Cell Organization ◽  
Viral Lifecycle

Viruses remodel cellular compartments to build their replication factories. Remarkably, viruses are also able to induce new membranes and new organelles. As a result of recent advances in light and transmission electron microscopy (TEM), we are starting to become aware of the variety of structures that viruses assemble inside cells. Viral factories are intracellular compartments harboring replication organelles that contain viral replication complexes and the sites of virus particle assembly. This lecture will revise the most relevant imaging technologies for studying the biogenesis of viral replication factories. Live cell microscopy, correlative light and electron microscopy, cryo-TEM, and three-dimensional imaging methods are unveiling how viruses manipulate cell organization. In particular, methods for molecular mapping in situ, in two and three dimensions, are revealing how macromolecular complexes build functional replication complexes inside infected cells. The combination of all these imaging approaches is uncovering the viral lifecycle events with a detail never seen before.

Turbulent three-dimensional dielectric electrohydrodynamic convection between two plates

2012 ◽  
Vol 696 ◽  
pp. 228-262 ◽  
Author(s):  
A. Kourmatzis ◽  
J. S. Shrimpton
Keyword(s):  
Spatial Data ◽  
Three Dimensional ◽  
Reynolds Numbers ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Energy Budgets ◽  
Turbulent Regime ◽  
Scalar Flux ◽  
Wide Range ◽  
Scalar Variance

AbstractThe fundamental mechanisms responsible for the creation of electrohydrodynamically driven roll structures in free electroconvection between two plates are analysed with reference to traditional Rayleigh–Bénard convection (RBC). Previously available knowledge limited to two dimensions is extended to three-dimensions, and a wide range of electric Reynolds numbers is analysed, extending into a fully inherently three-dimensional turbulent regime. Results reveal that structures appearing in three-dimensional electrohydrodynamics (EHD) are similar to those observed for RBC, and while two-dimensional EHD results bear some similarities with the three-dimensional results there are distinct differences. Analysis of two-point correlations and integral length scales show that full three-dimensional electroconvection is more chaotic than in two dimensions and this is also noted by qualitatively observing the roll structures that arise for both low (${\mathit{Re}}_{E} = 1$) and high electric Reynolds numbers (up to ${\mathit{Re}}_{E} = 120$). Furthermore, calculations of mean profiles and second-order moments along with energy budgets and spectra have examined the validity of neglecting the fluctuating electric field ${ E}_{i}^{\ensuremath{\prime} } $ in the Reynolds-averaged EHD equations and provide insight into the generation and transport mechanisms of turbulent EHD. Spectral and spatial data clearly indicate how fluctuating energy is transferred from electrical to hydrodynamic forms, on moving through the domain away from the charging electrode. It is shown that ${ E}_{i}^{\ensuremath{\prime} } $ is not negligible close to the walls and terms acting as sources and sinks in the turbulent kinetic energy, turbulent scalar flux and turbulent scalar variance equations are examined. Profiles of hydrodynamic terms in the budgets resemble those in the literature for RBC; however there are terms specific to EHD that are significant, indicating that the transfer of energy in EHD is also attributed to further electrodynamic terms and a strong coupling exists between the charge flux and variance, due to the ionic drift term.

scholarly journals Protocol for preparation of heterogeneous biological samples for 3D electron microscopy: a case study for insects

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alexey A. Polilov ◽  
Anastasia A. Makarova ◽  
Song Pang ◽  
C. Shan Xu ◽  
Harald Hess
Keyword(s):  
Electron Microscopy ◽  
Biological Samples ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Three Dimensional ◽  
Entire Volume ◽  
Simple Protocol ◽  
3D Electron Microscopy ◽  
3D Em

AbstractModern morphological and structural studies are coming to a new level by incorporating the latest methods of three-dimensional electron microscopy (3D-EM). One of the key problems for the wide usage of these methods is posed by difficulties with sample preparation, since the methods work poorly with heterogeneous (consisting of tissues different in structure and in chemical composition) samples and require expensive equipment and usually much time. We have developed a simple protocol allows preparing heterogeneous biological samples suitable for 3D-EM in a laboratory that has a standard supply of equipment and reagents for electron microscopy. This protocol, combined with focused ion-beam scanning electron microscopy, makes it possible to study 3D ultrastructure of complex biological samples, e.g., whole insect heads, over their entire volume at the cellular and subcellular levels. The protocol provides new opportunities for many areas of study, including connectomics.

scholarly journals Nervous Activity of the Brain in Five Dimensions

Biophysica ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 38-47
Author(s):  
Arturo Tozzi ◽  
James F. Peters ◽  
Norbert Jausovec ◽  
Arjuna P. H. Don ◽  
Sheela Ramanna ◽  
...  
Keyword(s):  
Fourier Analysis ◽  
Nervous Activity ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Data Sets ◽  
Spatial And Temporal Patterns ◽  
Five Dimensions ◽  
Four Dimensions ◽  
Scale Free ◽  
The Brain

The nervous activity of the brain takes place in higher-dimensional functional spaces. It has been proposed that the brain might be equipped with phase spaces characterized by four spatial dimensions plus time, instead of the classical three plus time. This suggests that global visualization methods for exploiting four-dimensional maps of three-dimensional experimental data sets might be used in neuroscience. We asked whether it is feasible to describe the four-dimensional trajectories (plus time) of two-dimensional (plus time) electroencephalographic traces (EEG). We made use of quaternion orthographic projections to map to the surface of four-dimensional hyperspheres EEG signal patches treated with Fourier analysis. Once achieved the proper quaternion maps, we show that this multi-dimensional procedure brings undoubted benefits. The treatment of EEG traces with Fourier analysis allows the investigation the scale-free activity of the brain in terms of trajectories on hyperspheres and quaternionic networks. Repetitive spatial and temporal patterns undetectable in three dimensions (plus time) are easily enlightened in four dimensions (plus time). Further, a quaternionic approach makes it feasible to identify spatially far apart and temporally distant periodic trajectories with the same features, such as, e.g., the same oscillatory frequency or amplitude. This leads to an incisive operational assessment of global or broken symmetries, domains of attraction inside three-dimensional projections and matching descriptions between the apparently random paths hidden in the very structure of nervous fractal signals.

Diagnosis of COVID-19 using 3D CT scans and vaccination for COVID-19

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Gangadhar Ch ◽  
S. Jana ◽  
Sankararao Majji ◽  
Prathyusha Kuncha ◽  
Fantin Irudaya Raj E. ◽  
...  
Keyword(s):  
Virus Isolate ◽  
Research Work ◽  
Three Dimensional ◽  
Ct Scans ◽  
Data Sets ◽  
Content Type ◽  
Infected People ◽  
3D Data ◽  
Ct Classification ◽  
First Time

Purpose For the first time in a decade, a new form of pneumonia virus, coronavirus, COVID-19, appeared in Wuhan, China. To date, it has affected millions of people, killed thousands and resulted in thousands of deaths around the world. To stop the spread of this virus, isolate the infected people. Computed tomography (CT) imaging is very accurate in revealing the details of the lungs and allows oncologists to detect COVID. However, the analysis of CT scans, which can include hundreds of images, may cause delays in hospitals. The use of artificial intelligence (AI) in radiology could help to COVID-19-positive cancer in this manner is the main purpose of the work. Design/methodology/approach CT scans are a medical imaging procedure that gives a three-dimensional (3D) representation of the lungs for clinical purposes. The volumetric 3D data sets can be regarded as axial, coronal and transverse data sets. By using AI, we can diagnose the virus presence. Findings The paper discusses the use of an AI for COVID-19, and CT classification issue and vaccination details of COVID-19 have been detailed in this paper. Originality/value Originality of the work is, all the data can be collected genuinely and did research work doneown methodology.

scholarly journals Ultrastructural Characterization of Flashing Mitochondria

Contact ◽  
2018 ◽  
Vol 1 ◽  
pp. 251525641880142
Author(s):  
Manon Rosselin ◽  
Paula Nunes-Hasler ◽  
Nicolas Demaurex
Keyword(s):  
Electron Microscopy ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Light And Electron Microscopy ◽  
Three Dimensional ◽  
Volume Ratio ◽  
Tubular Structures ◽  
Membrane Contact Sites ◽  
Contact Sites ◽  
Membrane Contact

Mitochondria undergo spontaneous transient elevations in matrix pH associated with drops in mitochondrial membrane potential. These mitopHlashes require a functional respiratory chain and the profusion protein optic atrophy 1, but their mechanistic basis is unclear. To gain insight on the origin of these dynamic events, we resolved the ultrastructure of flashing mitochondria by correlative light and electron microscopy. HeLa cells expressing the matrix-targeted pH probe mitoSypHer were screened for mitopHlashes and fixed immediately after the occurrence of a flashing event. The cells were then processed for imaging by serial block face scanning electron microscopy using a focused ion beam to generate ∼1,200 slices of 10 nm thickness from a 28 µm × 15 µm cellular volume. Correlation of live/fixed fluorescence and electron microscopy images allowed the unambiguous identification of flashing and nonflashing mitochondria. Three-dimensional reconstruction and surface mapping revealed that each tomogram contained two flashing mitochondria of unequal sizes, one being much larger than the average mitochondrial volume. Flashing mitochondria were 10-fold larger than silent mitochondria but with a surface to volume ratio and a cristae volume similar to nonflashing mitochondria. Flashing mitochondria were connected by tubular structures, formed more membrane contact sites, and a constriction was observed at a junction between a flashing mitochondrion and a nonflashing mitochondrion. These data indicate that flashing mitochondria are structurally preserved and bioenergetically competent but form numerous membrane contact sites and are connected by tubular structures, consistent with our earlier suggestion that mitopHlashes might be triggered by the opening of fusion pores between contiguous mitochondria.

scholarly journals 3-DIMENSIONAL GEOLOGICAL MAPPING AND MODELING ACTIVITIES AT THE GEOLOGICAL SURVEY OF NORWAY

2015 ◽  
Vol XL-2/W4 ◽  
pp. 11-16 ◽  
Author(s):  
A. Jarna ◽  
A. Bang-Kittilsen ◽  
C. Haase ◽  
I. H. C. Henderson ◽  
F. Høgaas ◽  
...  
Keyword(s):  
3D Visualization ◽  
Three Dimensional ◽  
Mineral Resources ◽  
Geological Mapping ◽  
Geological Survey ◽  
Marine Geology ◽  
Data Infrastructure ◽  
3 Dimensional ◽  
3D Data ◽  
Wide Range

Geology and all geological structures are three-dimensional in space. Geology can be easily shown as four-dimensional when time is considered. Therefore GIS, databases, and 3D visualization software are common tools used by geoscientists to view, analyse, create models, interpret and communicate geological data. The NGU (Geological Survey of Norway) is the national institution for the study of bedrock, mineral resources, surficial deposits and groundwater and marine geology. The interest in 3D mapping and modelling has been reflected by the increase of number of groups and researches dealing with 3D in geology within NGU. This paper highlights 3D geological modelling techniques and the usage of these tools in bedrock, geophysics, urban and groundwater studies at NGU, same as visualisation of 3D online. The examples show use of a wide range of data, methods, software and an increased focus on interpretation and communication of geology in 3D. The goal is to gradually expand the geospatial data infrastructure to include 3D data at the same level as 2D.

scholarly journals Dynamics of in vivo ASC speck formation

2017 ◽  
Vol 216 (9) ◽  
pp. 2891-2909 ◽  
Author(s):  
Paola Kuri ◽  
Nicole L. Schieber ◽  
Thomas Thumberger ◽  
Joachim Wittbrodt ◽  
Yannick Schwab ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Cell Death ◽  
Light And Electron Microscopy ◽  
Three Dimensional ◽  
Inflammasome Activation ◽  
Caspase Activation ◽  
Endogenous Gene ◽  
Pyrin Domain ◽  
Effector Caspase

Activated danger or pathogen sensors trigger assembly of the inflammasome adaptor ASC into specks, large signaling platforms considered hallmarks of inflammasome activation. Because a lack of in vivo tools has prevented the study of endogenous ASC dynamics, we generated a live ASC reporter through CRISPR/Cas9 tagging of the endogenous gene in zebrafish. We see strong ASC expression in the skin and other epithelia that act as barriers to insult. A toxic stimulus triggered speck formation and rapid pyroptosis in keratinocytes in vivo. Macrophages engulfed and digested that speck-containing, pyroptotic debris. A three-dimensional, ultrastructural reconstruction, based on correlative light and electron microscopy of the in vivo assembled specks revealed a compact network of highly intercrossed filaments, whereas pyrin domain (PYD) or caspase activation and recruitment domain alone formed filamentous aggregates. The effector caspase is recruited through PYD, whose overexpression induced pyroptosis but only after substantial delay. Therefore, formation of a single, compact speck and rapid cell-death induction in vivo requires a full-length ASC.

scholarly journals The magnetorotational instability prefers three dimensions

2020 ◽  
Vol 476 (2233) ◽  
pp. 20190622
Author(s):  
Jeffrey S. Oishi ◽  
Geoffrey M. Vasil ◽  
Morgan Baxter ◽  
Andrew Swan ◽  
Keaton J. Burns ◽  
...  
Keyword(s):  
Shear Rate ◽  
Angular Velocity ◽  
Laboratory Experiments ◽  
Three Dimensional ◽  
Linear Instability ◽  
Three Dimensions ◽  
Two Dimensional ◽  
Magnetorotational Instability ◽  
Dynamo Action ◽  
Wide Range

The magnetorotational instability (MRI) occurs when a weak magnetic field destabilizes a rotating, electrically conducting fluid with inwardly increasing angular velocity. The MRI is essential to astrophysical disc theory where the shear is typically Keplerian. Internal shear layers in stars may also be MRI-unstable, and they take a wide range of profiles, including near-critical. We show that the fastest growing modes of an ideal magnetofluid are three-dimensional provided the shear rate, S , is near the two-dimensional onset value, S c . For a Keplerian shear, three-dimensional modes are unstable above S  ≈ 0.10 S c , and dominate the two-dimensional modes until S  ≈ 2.05 S c . These three-dimensional modes dominate for shear profiles relevant to stars and at magnetic Prandtl numbers relevant to liquid-metal laboratory experiments. Significant numbers of rapidly growing three-dimensional modes remainy well past 2.05 S c . These finding are significant in three ways. First, weakly nonlinear theory suggests that the MRI saturates by pushing the shear rate to its critical value. This can happen for systems, such as stars and laboratory experiments, that can rearrange their angular velocity profiles. Second, the non-normal character and large transient growth of MRI modes should be important whenever three-dimensionality exists. Finally, three-dimensional growth suggests direct dynamo action driven from the linear instability.

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