scholarly journals Identifying Long-range Synaptic Inputs Using Genetically Encoded Labels and Volume Electron Microscopy

2022 ◽  
Author(s):  
Irene P. Ayuso-Jimeno ◽  
Paolo Ronchi ◽  
Tianzi Wang ◽  
Catherine Gallori ◽  
Cornelius T. Gross
Keyword(s):  
Electron Microscopy ◽  
Long Range ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Anterior Cingulate ◽  
Specific Cell ◽  
Reaction Products ◽  
Synaptic Inputs ◽  
Surfactant Treatment ◽  
Volume Em

Abstract Enzymes that facilitate the local deposition of electron dense reaction products have been widely used as labels in electron microscopy (EM). Peroxidases, in particular, can efficiently metabolize 3,3′-diaminobenzidine tetrahydrochloride hydrate (DAB) to produce precipitates with high contrast under EM following heavy metal staining, and can be genetically encoded to facilitate the labeling of specific cell-types or organelles. Nevertheless, the peroxidase/DAB method has so far not been reported to work in combination with 3D volume EM techniques (e.g. Serial blockface electron microscopy, SBEM; Focused ion beam electron microscopy, FIBSEM) because the surfactant treatment needed for efficient reagent penetration disrupts tissue ultrastructure and because these methods require the deposition of large amounts of heavy metals that can obscure DAB precipitates. However, a recently described peroxidase with enhanced enzymatic activity (dAPEX2) appears to successfully deposit EM-visible DAB products in thick tissue without surfactant treatment. Here we demonstrate that multiplexed dAPEX2/DAB tagging is compatible with both FIBSEM and SBEM volume EM approaches and use them to map long-range genetically identified synaptic inputs from the anterior cingulate cortex to the periaqueductal gray in the mouse brain.

scholarly journals Identifying long-range synaptic inputs using genetically encoded labels and volume electron microscopy

2021 ◽  
Author(s):  
Irene Pilar Ayuso Jimeno ◽  
Paolo Ronchi ◽  
Tianzi Wang ◽  
Catherine Gallori ◽  
Cornelius Thilo Gross
Keyword(s):  
Electron Microscopy ◽  
Long Range ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Anterior Cingulate ◽  
Specific Cell ◽  
Reaction Products ◽  
Synaptic Inputs ◽  
Surfactant Treatment ◽  
Volume Em

Enzymes that facilitate the local deposition of electron dense reaction products have been widely used as labels in electron microscopy (EM). Peroxidases, in particular, can efficiently metabolize 3,3′-diaminobenzidine tetrahydrochloride hydrate (DAB) to produce precipitates with high contrast under EM following heavy metal staining, and can be genetically encoded to facilitate the labeling of specific cell-types or organelles. Nevertheless, the peroxidase/DAB method has so far not been reported to work in combination with 3D volume EM techniques (e.g. Serial blockface electron microscopy, SBEM; Focused ion beam electron microscopy, FIBSEM) because the surfactant treatment needed for efficient reagent penetration disrupts tissue ultrastructure and because these methods require the deposition of large amounts of heavy metals that can obscure DAB precipitates. However, a recently described peroxidase with enhanced enzymatic activity (dAPEX2) appears to successfully deposit EM-visible DAB products in thick tissue without surfactant treatment. Here we demonstrate that multiplexed dAPEX2/DAB tagging is compatible with both FIBSEM and SBEM volume EM approaches and use them to map long-range genetically identified synaptic inputs from the anterior cingulate cortex to the periaqueductal gray in the mouse brain.

scholarly journals FIB-SEM as a Volume Electron Microscopy Approach to Study Cellular Architectures in SARS-CoV-2 and Other Viral Infections: A Practical Primer for a Virologist

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 611
Author(s):  
Valentina Baena ◽  
Ryan Conrad ◽  
Patrick Friday ◽  
Ella Fitzgerald ◽  
Taeeun Kim ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Focused Ion Beam ◽  
Viral Infections ◽  
Ion Beam ◽  
In Vitro Study ◽  
Wide Range ◽  
Sem Imaging ◽  
Volume Electron Microscopy ◽  
Volume Em

The visualization of cellular ultrastructure over a wide range of volumes is becoming possible by increasingly powerful techniques grouped under the rubric “volume electron microscopy” or volume EM (vEM). Focused ion beam scanning electron microscopy (FIB-SEM) occupies a “Goldilocks zone” in vEM: iterative and automated cycles of milling and imaging allow the interrogation of microns-thick specimens in 3-D at resolutions of tens of nanometers or less. This bestows on FIB-SEM the unique ability to aid the accurate and precise study of architectures of virus-cell interactions. Here we give the virologist or cell biologist a primer on FIB-SEM imaging in the context of vEM and discuss practical aspects of a room temperature FIB-SEM experiment. In an in vitro study of SARS-CoV-2 infection, we show that accurate quantitation of viral densities and surface curvatures enabled by FIB-SEM imaging reveals SARS-CoV-2 viruses preferentially located at areas of plasma membrane that have positive mean curvatures.

Tem Investigation of Phases Formed During Aluminium Wetting of MgO at [100], [110] and [111] Orientations

2013 ◽  
Vol 58 (2) ◽  
pp. 497-500 ◽  
Author(s):  
J. Morgiel ◽  
N. Sobczak ◽  
M. Pomorska ◽  
R. Nowak ◽  
J. Wojewoda-Budka
Keyword(s):  
Electron Microscopy ◽  
Focused Ion Beam ◽  
Sessile Drop ◽  
Ion Beam ◽  
Reaction Products ◽  
Liquid Aluminium ◽  
Coarse Dendrite ◽  
Thin Foils ◽  
Transmission Electron ◽  
Diffraction Patterns

The interaction of liquid aluminium (5N) with single crystal MgO substrates of [100], [110] and [111] orientations (surface roughness <1 nm) were studied using sessile drop wettability test performed at 1000ºC for 1 hour in vacuum (5 x 10-6 mbar). The observations performed using scanning electron microscopy (SEM) showed that the interaction of liquid metal with MgO crystals in all cases resulted in the formation of reaction products region (RPR) of thickness varying from ∽40 up to ∽80 microns in depth. In each case the RPR consisted mainly of coarse dendrite-like crystallites of few microns thick surrounded by net of much thinner channels. Occasionally away from the RPR centre the areas built of much finner but also dendrite- or filament-like crystallites were noted. The thin foils for transmission electron microscopy (TEM) investigations were cut using focused ion beam system (FIB) both from drop/RPR as well as RPR/MgO interfacial regions. The electron diffractions proved that the dominating coarse dendrite-like crystallites are of the same α-Al2O3 type throughout the whole RPR for all substrates orientations. Similarly, the colonies of finer crystallites always showed diffraction patterns characteristic for MgAl2O4 spinel. Therefore, the performed investigation indicated, that both the reaction layer depth and the reaction path represented by the sequence and type of phases present in Al/MgO RPR remain roughly similar for all examined orientations, i.e. that the substrate orientation control neither reaction kinetics, nor affects final phase composition of RPR.

TEM Sample Preparation Tricks for Advanced DRAMs

2015 ◽  
Author(s):  
Ching Shan Sung ◽  
Hsiu Ting Lee ◽  
Jian Shing Luo
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Sample Preparation ◽  
Integrated Circuit ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Tem Analysis ◽  
Cross Sectional ◽  
Transmission Electron ◽  
Characterization Of Materials

Abstract Transmission electron microscopy (TEM) plays an important role in the structural analysis and characterization of materials for process evaluation and failure analysis in the integrated circuit (IC) industry as device shrinkage continues. It is well known that a high quality TEM sample is one of the keys which enables to facilitate successful TEM analysis. This paper demonstrates a few examples to show the tricks on positioning, protection deposition, sample dicing, and focused ion beam milling of the TEM sample preparation for advanced DRAMs. The micro-structures of the devices and samples architectures were observed by using cross sectional transmission electron microscopy, scanning electron microscopy, and optical microscopy. Following these tricks can help readers to prepare TEM samples with higher quality and efficiency.

Fin Level Defect Isolation Inside a FinFET Using Electron Beam Alteration of Current Flow

2017 ◽  
Author(s):  
H.J. Ryu ◽  
A.B. Shah ◽  
Y. Wang ◽  
W.-H. Chuang ◽  
T. Tong
Keyword(s):  
Electron Microscopy ◽  
Electron Beam ◽  
Focused Ion Beam ◽  
Current Flow ◽  
Ion Beam ◽  
The Body ◽  
Complete Understanding ◽  
Root Cause ◽  
Transmission Electron ◽  
Defect Isolation

Abstract When failure analysis is performed on a circuit composed of FinFETs, the degree of defect isolation, in some cases, requires isolation to the fin level inside the problematic FinFET for complete understanding of root cause. This work shows successful application of electron beam alteration of current flow combined with nanoprobing for precise isolation of a defect down to fin level. To understand the mechanism of the leakage, transmission electron microscopy (TEM) slice was made along the leaky drain contact (perpendicular to fin direction) by focused ion beam thinning and lift-out. TEM image shows contact and fin. Stacking fault was found in the body of the silicon fin highlighted by the technique described in this paper.

Transmission Electron Microscopy (TEM) Specimen Preparation Technique using Focused Ion Beam (FIB): Application to Material Characterization of Chemical Vapor Deposition of Tungsten (W) and Tungsten Silicides (WSix)

1997 ◽  
Author(s):  
K. Doong ◽  
J.-M. Fu ◽  
Y.-C. Huang
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Chemical Vapor Deposition ◽  
Vapor Deposition ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Chemical Vapor ◽  
Specimen Preparation ◽  
Preparation Technique ◽  
Transmission Electron

Abstract The specimen preparation technique using focused ion beam (FIB) to generate cross-sectional transmission electron microscopy (XTEM) samples of chemical vapor deposition (CVD) of Tungsten-plug (W-plug) and Tungsten Silicides (WSix) was studied. Using the combination method including two axes tilting[l], gas enhanced focused ion beam milling[2] and sacrificial metal coating on both sides of electron transmission membrane[3], it was possible to prepare a sample with minimal thickness (less than 1000 A) to get high spatial resolution in TEM observation. Based on this novel thinning technique, some applications such as XTEM observation of W-plug with different aspect ratio (I - 6), and the grain structure of CVD W-plug and CVD WSix were done. Also the problems and artifacts of XTEM sample preparation of high Z-factor material such as CVD W-plug and CVD WSix were given and the ways to avoid or minimize them were suggested.

A Methodology to Reduce Ion Beam Induced Damage in TEM Specimens Prepared by FIB

2002 ◽  
Author(s):  
Chin Kai Liu ◽  
Chi Jen. Chen ◽  
Jeh Yan.Chiou ◽  
David Su
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Sample Preparation ◽  
Integrated Circuit ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Specimen Preparation ◽  
Tem Analysis ◽  
Sensitive Issue ◽  
Transmission Electron

Abstract Focused ion beam (FIB) has become a useful tool in the Integrated Circuit (IC) industry, It is playing an important role in Failure Analysis (FA), circuit repair and Transmission Electron Microscopy (TEM) specimen preparation. In particular, preparation of TEM samples using FIB has become popular within the last ten years [1]; the progress in this field is well documented. Given the usefulness of FIB, “Artifact” however is a very sensitive issue in TEM inspections. The ability to identify those artifacts in TEM analysis is an important as to understanding the significance of pictures In this paper, we will describe how to measure the damages introduced by FIB sample preparation and introduce a better way to prevent such kind of artifacts.

BiCMOS Die Sort Yield Improvement from Isolation of a Localized Defect Mechanism and Precision TEM Cross Section

1997 ◽  
Author(s):  
J. Douglass ◽  
T. D. Myers ◽  
F. Tsai ◽  
R. Ketcheson ◽  
J. Errett
Keyword(s):  
Electron Microscopy ◽  
Cross Section ◽  
Focused Ion Beam ◽  
Yield Loss ◽  
Process Analysis ◽  
Ion Beam ◽  
Yield Improvement ◽  
Transmission Electron ◽  
Defect Mechanism ◽  
Water Residue

Abstract This paper describes how the authors used a combination of focused ion beam (FIB) microprobing, transmission electron microscopy (TEM), and data and process analysis to determine that localized water residue was causing a 6% yield loss at die sort.

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.

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