A multiresolution approach to the 3D reconstruction of a 50S ribosome from an EM-tilt series solving the alignment problem without gold particles (electron microscopy)

2002 ◽  
Author(s):  
M. Cop ◽  
J. Dengler
Keyword(s):  
Electron Microscopy ◽  
3D Reconstruction ◽  
Gold Particles ◽  
Alignment Problem ◽  
Tilt Series

Ultrastructural analysis of the spatial distribution of MRNA

1992 ◽  
Vol 50 (1) ◽  
pp. 552-553
Author(s):  
Gary Bassell ◽  
Robert H. Singer
Keyword(s):  
Electron Microscopy ◽  
Spatial Distribution ◽  
In Situ Hybridization ◽  
High Resolution ◽  
Nucleic Acids ◽  
Colloidal Gold ◽  
Dna Probe ◽  
Nucleotide Analogs ◽  
Gold Particles

We have been investigating the spatial distribution of nucleic acids intracellularly using in situ hybridization. The use of non-isotopic nucleotide analogs incorporated into the DNA probe allows the detection of the probe at its site of hybridization within the cell. This approach therefore is compatible with the high resolution available by electron microscopy. Biotinated or digoxigenated probe can be detected by antibodies conjugated to colloidal gold. Because mRNA serves as a template for the probe fragments, the colloidal gold particles are detected as arrays which allow it to be unequivocally distinguished from background.

Specificity of Lectins Labeled with Colloidal Gold to the Exopolymeric Matrix Carbohydrates of the Sulfate-Reducing Bacteria Biofilm Formed on Steel

2020 ◽  
Vol 82 (5) ◽  
pp. 11-20
Author(s):  
D.R. Abdulina ◽  
◽  
L.M. Purish ◽  
G.O. Iutynska ◽  
◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Colloidal Gold ◽  
Steel Surface ◽  
Lectin Binding ◽  
Sulfate Reducing Bacteria ◽  
Gold Particles ◽  
Sulfate Reducing ◽  
Transmission Electron ◽  
Reducing Bacteria

The studies of the carbohydrate composition of the sulfate-reducing bacteria (SRB) biofilms formed on the steel surface, which are a factor of microbial corrosion, are significant. Since exopolymers synthesized by bacteria could activate corrosive processes. The aim of the study was to investigate the specificity of commercial lectins, labeled with colloidal gold to carbohydrates in the biofilm exopolymeric matrix produced by the corrosive-relevant SRB strains from man-caused ecotopes. Methods. Microbiological methods (obtaining of the SRB biofilms during cultivation in liquid Postgate B media under microaerophilic conditions), biochemical methods (lectin-binding analysis of 10 commercial lectins, labeled with colloidal gold), transmission electron microscopy using JEM-1400 JEOL. Results. It was shown using transmission electron microscopy that the binding of lectins with carbohydrates in the biofilm of the studied SRB strains occurred directly in the exopolymerіс matrix, as well as on the surfaces of bacterial cells, as seen by the presence of colloidal gold particles. For detection of the neutral carbohydrates (D-glucose and D-mannose) in the biofilm of almost all studied bacterial strains PSA lectin was the most specific. This lectin binding in biofilms of Desulfotomaculum sp. К1/3 and Desulfovibrio sp. 10 strains was higher in 90.8% and 94.4%, respectively, then for ConA lectin. The presence of fucose in the SRB biofilms was detected using LABA lectin, that showed specificity to the biofilm EPS of all the studied strains. LBA lectin was the most specific to N-аcetyl-D-galactosamine for determination of amino sugars in the biofilm. The amount of this lectin binding in D. vulgaris DSM644 biofilm was 30.3, 10.1 and 9.3 times higher than SBA, SNA and PNA lectins, respectively. STA, LVA and WGA lectins were used to detect the N-acetyl-Dglucosamine and sialic acid in the biofilm. WGA lectin showed specificity to N-acetyl-D-glucosamine in the biofilm of all the studied SRB; maximum number of bounded colloidal gold particles (175 particles/μm2) was found in the Desulfotomaculum sp. TC3 biofilm. STA lectin was interacted most actively with N-acetyl-D-glucosamine in Desulfotomaculum sp. TC3 and Desulfomicrobium sp. TC4 biofilms. The number of bounded colloidal gold particles was in 9.2 and 7.4 times higher, respectively, than using LVA lectin. The lowest binding of colloidal gold particles was observed for LVA lectin. Conclusions. It was identified the individual specificity of the 10 commercial lectins to the carbohydrates of biofilm matrix on the steel surface, produced by SRB. It was estimated that lectins with identical carbohydrates specificity had variation in binding to the biofilm carbohydrates of different SRB strains. Establishing of the lectin range selected for each culture lead to the reduction of the scope of studies and labor time in the researching of the peculiarities of exopolymeric matrix composition of biofilms formed by corrosiverelevant SRB.

Embedded Gold Markers for Improved TEM/STEM Tomography Reconstruction

2008 ◽  
Author(s):  
Jian-Shing Luo ◽  
Chia-Chi Huang ◽  
Jeremy D. Russell
Keyword(s):  
3D Reconstruction ◽  
Feature Tracking ◽  
Semiconductor Device ◽  
Electron Tomography ◽  
Tracking Process ◽  
Carbon Coated ◽  
Novel Method ◽  
Tomography Reconstruction ◽  
Tilt Series ◽  
20 Nm

Abstract Electron tomography includes four main steps: tomography data acquisition, image processing, 3D reconstruction, and visualization. After acquisition, tilt-series alignments are performed. Two methods are used to align the tilt-series: cross-correlation and feature tracking. Normally, about 10-20 nm of fiducial markers, such as gold beads, are deposited onto one side of 100 mesh carbon-coated grids during the feature-tracking process. This paper presents a novel method for preparing electron tomography samples with gold beads inside to improve the feature tracking process and quality of 3D reconstruction. Results show that the novel electron tomography sample preparation method improves image alignment, which is essential for successful tomography in many contemporary semiconductor device structures.

scholarly journals Development of High-Throughput, High-Resolution 3D Reconstruction of Large-Volume Biological Tissue Using Automated Tape Collection Ultramicrotomy and Scanning Electron Microscopy

2011 ◽  
Vol 17 (S2) ◽  
pp. 966-967 ◽  
Author(s):  
R Schalek ◽  
N Kasthuri ◽  
K Hayworth ◽  
D Berger ◽  
J Tapia ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
High Resolution ◽  
3D Reconstruction ◽  
High Throughput ◽  
Large Volume ◽  
Biological Tissue ◽  
Scanning Electron

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

Colloidal gold particles as a new in vivo marker of early acute lung injury

2004 ◽  
Vol 287 (4) ◽  
pp. L867-L878 ◽  
Author(s):  
Kai Heckel ◽  
Rainer Kiefmann ◽  
Martina Dörger ◽  
Mechthild Stoeckelhuber ◽  
Alwin E. Goetz
Keyword(s):  
Electron Microscopy ◽  
Acute Lung Injury ◽  
Gas Exchange ◽  
Lung Injury ◽  
Colloidal Gold ◽  
Microvascular Permeability ◽  
Arterial Oxygen ◽  
Control Group ◽  
Gold Particles

Permeability of the endothelial barrier to large molecules plays a pivotal role in the manifestation of early acute lung injury. We present a novel and sensitive technique that brings microanatomical visualization and quantification of microvascular permeability in line. White New Zealand rabbits were anesthetized and ventilated mechanically. Rabbit serum albumin (RSA) was labeled with colloidal gold particles. We quantified macromolecular leakage of gold-labeled RSA and thickening of the gas exchange distance by electron microscopy, taking into account morphology of microvessels. The control group receiving a saline solution represented a normal gas exchange barrier without extravasation of gold-labeled albumin. Infusion of lipopolysaccharide (LPS) resulted in a significant displacement of gold-labeled albumin into pulmonary cells, the lung interstitium, and even the alveolar space. Correspondingly, intravital fluorescence microscopy and digital image analysis indicated thickening of width of alveolar septa. The findings were accompanied by a deterioration of alveolo-arterial oxygen difference, whereas wet/dry ratio and albumin concentration in the bronchoalveolar lavage fluid failed to detect that early stage of pulmonary edema. Inhibition of the nuclear enzyme poly(ADP-ribose) synthetase by 3-aminobenzamide prevented LPS-induced microvascular injury. To summarize: colloidal gold particles visualized by standard electron microscopy are a new and very sensitive in vivo marker of microvascular permeability in early acute lung injury. This technique enabling detailed microanatomical and quantitative pathophysiological characterization of edema formation can form the basis for evaluating novel treatment strategies against acute lung injury.

scholarly journals In situ structure determination using single particle cryo-electron microscopy images

2020 ◽  
Author(s):  
Jing Cheng ◽  
Bufan Li ◽  
Long Si ◽  
Xinzheng Zhang
Keyword(s):  
Electron Microscopy ◽  
Structure Determination ◽  
Single Particle ◽  
Structure Refinement ◽  
Target Function ◽  
Target Protein ◽  
Particle Analysis ◽  
Cryo Electron Microscopy ◽  
Tilt Series

AbstractCryo-electron microscopy (cryo-EM) tomography is a powerful tool for in situ structure determination. However, this method requires the acquisition of tilt series, and its time consuming throughput of acquiring tilt series severely slows determination of in situ structures. By treating the electron densities of non-target protein as non-Gaussian distributed noise, we developed a new target function that greatly improves the efficiency of the recognition of the target protein in a single cryo-EM image without acquiring tilt series. Moreover, we developed a sorting function that effectively eliminates the false positive detection, which not only improves the resolution during the subsequent structure refinement procedure but also allows using homolog proteins as models to recognize the target protein. Together, we developed an in situ single particle analysis (isSPA) method. Our isSPA method was successfully applied to solve structures of glycoproteins on the surface of a non-icosahedral virus and Rubisco inside the carboxysome. The cryo-EM data from both samples were collected within 24 hours, thus allowing fast and simple structural determination in situ.

scholarly journals Preparation of Protein a Gold

1997 ◽  
Vol 5 (5) ◽  
pp. 12-13
Author(s):  
Paul Webster
Keyword(s):  
Electron Microscopy ◽  
Biological Activity ◽  
Colloidal Gold ◽  
Protein A ◽  
List Type ◽  
Type Number ◽  
Stained Glass ◽  
Small Particles ◽  
Silver Enhancement ◽  
Gold Particles

Colloidal gold has been used for centuries in the preparation of stained glass for windows and fine glassware. In recent years, colloidal gold particles have become a useful tool in microscopy for staining tissues and sections. Colloidal gold particles are especially useful for biological electron microscopy, Some of the reasons why are listed below.*Homogeneous preparations of particles varying in size from 3μm to 20μm can be easily prepared.*Colloidal gold suspensions are inexpensive to prepare. Most proteins can be easily coupled to colloidal gold particles.*Most proteins can be easily coupled to colloidal gold particles.*Proteins coupled to gold particles do not appear to lose their biological activity.*The colloidal gold particles can be easily seen in the electron microscope.*Colloidal gold does not naturally occur in biological material. Therefore, if you see it, it is because you put it there.*Colloidal gold probes can be used for light microscopy, The larger gold particles can be directly observed by the light microscope. Small particles are detected by silver enhancement or epipolarized illumination.*The same probes can be used for both LM and TEM imrnunocytochemistry.

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