scholarly journals Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2126
Author(s):  
Victoria Turzynski ◽  
Indra Monsees ◽  
Cristina Moraru ◽  
Alexander J. Probst
Keyword(s):  
Environmental Samples ◽  
Imaging Techniques ◽  
Environmental Genomics ◽  
Host Interaction ◽  
Current State ◽  
Transmission Electron ◽  
Archaeal Viruses ◽  
Viral Particles ◽  
Global Biogeochemical Cycles ◽  
Biological Entities

Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses—bacteriophages and archaeal viruses—influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage–host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth’s ecosystems.

Application of Lattice Imaging Techniques to Amorphous Films

1975 ◽  
Vol 33 ◽  
pp. 8-9
Author(s):  
S. R. Herd ◽  
P. Chaudhari
Keyword(s):  
Nearest Neighbor ◽  
Random Network ◽  
Imaging Techniques ◽  
Network Models ◽  
Accurate Method ◽  
Direct Transmission ◽  
Lattice Imaging ◽  
Transmission Electron ◽  
Lattice Planes ◽  
Nearest Neighbor Distances

Electron diffraction and direct transmission have been used extensively to study the local atomic arrangement in amorphous solids and in particular Ge. Nearest neighbor distances had been calculated from E.D. profiles and the results have been interpreted in terms of the microcrystalline or the random network models. Direct transmission electron microscopy appears the most direct and accurate method to resolve this issue since the spacial resolution of the better instruments are of the order of 3Å. In particular the tilted beam interference method is used regularly to show fringes corresponding to 1.5 to 3Å lattice planes in crystals as resolution tests.

Recent applications of TEM to the study of interfaces

1990 ◽  
Vol 48 (4) ◽  
pp. 308-309
Author(s):  
C. Barry Carter
Keyword(s):  
High Resolution ◽  
Sample Preparation ◽  
Grain Boundaries ◽  
Diffuse Scattering ◽  
Imaging Techniques ◽  
Amorphous Material ◽  
Contrast Imaging ◽  
Current State ◽  
Actual Nature ◽  
High Resolution Images

This paper will review the current state of understanding of interface structure and highlight some of the future needs and problems which must be overcome. The study of this subject can be separated into three different topics: 1) the fundamental electron microscopy aspects, 2) material-specific features of the study and 3) the characteristics of the particular interfaces. The two topics which are relevant to most studies are the choice of imaging techniques and sample preparation. The techniques used to study interfaces in the TEM include high-resolution imaging, conventional diffraction-contrast imaging, and phase-contrast imaging (Fresnel fringe images, diffuse scattering). The material studied affects not only the characteristics of the interfaces (through changes in bonding, etc.) but also the method used for sample preparation which may in turn have a significant affect on the resulting image. Finally, the actual nature and geometry of the interface must be considered. For example, it has become increasingly clear that the plane of the interface is particularly important whenever at least one of the adjoining grains is crystalline.A particularly productive approach to the study of interfaces is to combine different imaging techniques as illustrated in the study of grain boundaries in alumina. In this case, the conventional imaging approach showed that most grain boundaries in ion-thinned samples are grooved at the grain boundary although the extent of this grooving clearly depends on the crystallography of the surface. The use of diffuse scattering (from amorphous regions) gives invaluable information here since it can be used to confirm directly that surface grooving does occur and that the grooves can fill with amorphous material during sample preparation (see Fig. 1). Extensive use of image simulation has shown that, although information concerning the interface can be obtained from Fresnel-fringe images, the introduction of artifacts through sample preparation cannot be lightly ignored. The Fresnel-fringe simulation has been carried out using a commercial multislice program (TEMPAS) which was intended for simulation of high-resolution images.

A combined pseudoreplica-immunocytochemical technique for research and diagnostic virology

1990 ◽  
Vol 48 (3) ◽  
pp. 900-901
Author(s):  
Blayne Fritz ◽  
Stanley J. Naides ◽  
Kenneth Moore
Keyword(s):  
Phosphotungstic Acid ◽  
Immunogold Labelling ◽  
Uranyl Acetate ◽  
Distilled Water ◽  
Clinical Specimens ◽  
Tissue Sections ◽  
Specimen Retrieval ◽  
Transmission Electron ◽  
Viral Particles ◽  
Diagnostic Virology

The pseudoreplica method of staining viral particles for visualization by transmission electron microscopy is a very popular technique. The ability to concentrate clinical specimens while semi-embedding viral particles makes it especially well suited for morphologic and diagnostic virology. Immunolabelling viral particles with colloidal gold is a technique frequently employed by both research and diagnostic virologists. We have characterized a procedure which provides the advantage of both by modifying and combining pseudoreplica staining and immunogold labelling.Modification of specimen retrieval and delay of staining allows us to utilize pseudoreplica processed specimens within our standard immunogold labelling protocol. In brief, we absorbed samples onto 2% agarose, added.25% Formvar and wicked dry. We then floated the Formvar-virus film onto double distilled water, added grids and retrieved with parafilm. The Formvar-virus specimens were then treated as thin tissue sections within our standard two stage immunolabelling protocol. Following completion of immunogold labelling; each grid was negatively stained with phosphotungstic acid or uranyl acetate contrast stains.

Separation of Extracellular Vesicles by DNA-Directed Immunocapturing Followed by Enzymatic Release

2020 ◽  
Author(s):  
Dario Brambilla ◽  
Laura Sola ◽  
Elisa Chiodi ◽  
Natasa Zarovni ◽  
Diogo Fortunato ◽  
...  
Keyword(s):  
Cell Culture ◽  
Extracellular Vesicles ◽  
Culture Media ◽  
Biological Fluids ◽  
Imaging Techniques ◽  
Cell Communication ◽  
Disease Diagnosis ◽  
Cell Culture Supernatant ◽  
Transmission Electron ◽  
Downstream Analysis

Extracellular vesicles (EVs) have attracted great interest among researchers due to their role in cell-cell communication, disease diagnosis, and drug delivery. In spite of their potential in the medical field, there is no consensus on the best method for separating microvesicles from cell culture supernatant and complex biological fluids. Obtaining a good recovery yield and preserving physical characteristics is critical for the diagnostic and therapeutic use of EVs. The separation is made complex by the fact that blood and cell culture media, contain a large number of nanoparticles in the same size range. Methods that exploit immunoaffinity capture provide high purity samples and overcome the issues of currently used separation methods. However, the release of captured nanovesicles requires harsh conditions that hinder their use in certain types of downstream analysis. Herein, a novel capture and release approach for small extracellular vesicles (sEVs), based on DNAdirected immobilization of antiCD63 antibody is presented. The flexible DNAlinker increases the capture efficiency and allows releasing of EVs by exploiting the endonucleasic activity of DNAse I. This separation protocol works under mild conditions, enabling the release of intact vesicles that can be successfully analyzed by imaging techniques. In this article sEVs recovered from plasma were characterized by established techniques for EVs analysis including nanoparticle tracking and transmission electron microscopy.<br>

scholarly journals Structural Analysis of Jumbo Coliphage phAPEC6

2020 ◽  
Vol 21 (9) ◽  
pp. 3119 ◽  
Author(s):  
Jeroen Wagemans ◽  
Jessica Tsonos ◽  
Dominique Holtappels ◽  
Kiandro Fortuna ◽  
Jean-Pierre Hernalsteens ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Capsid Protein ◽  
Tem Analysis ◽  
Host Interaction ◽  
Cryo Electron Microscopy ◽  
Transmission Electron ◽  
Tail Sheath ◽  
Associated Proteins ◽  
Contractile Tail ◽  
Phage Capsid

The phAPEC6 genome encodes 551 predicted gene products, with the vast majority (83%) of unknown function. Of these, 62 have been identified as virion-associated proteins by mass spectrometry (ESI-MS/MS), including the major capsid protein (Gp225; present in 1620 copies), which shows a HK97 capsid protein-based fold. Cryo-electron microscopy experiments showed that the 350-kbp DNA molecule of Escherichia coli virus phAPEC6 is packaged in at least 15 concentric layers in the phage capsid. A capsid inner body rod is also present, measuring about 91 nm by 18 nm and oriented along the portal axis. In the phAPEC6 contractile tail, 25 hexameric stacked rings can be distinguished, built of the identified tail sheath protein (Gp277). Cryo-EM reconstruction reveals the base of the unique hairy fibers observed during an initial transmission electron microscopy (TEM) analysis. These very unusual filaments are ordered at three annular positions along the contractile sheath, as well as around the capsid, and may be involved in host interaction.

scholarly journals Induction of Multiple Prophages from a Marine Bacterium: a Genomic Approach

2006 ◽  
Vol 72 (7) ◽  
pp. 4995-5001 ◽  
Author(s):  
Feng Chen ◽  
Kui Wang ◽  
Jeneen Stewart ◽  
Robert Belas
Keyword(s):  
Mitomycin C ◽  
Marine Bacterium ◽  
Pcr Amplification ◽  
Pulsed Field Gel Electrophoresis ◽  
Bacterial Genomes ◽  
Dominant Type ◽  
Transmission Electron ◽  
Viral Particles ◽  
Genomic Approach ◽  
Primer Sets

ABSTRACT Approximately 70% of sequenced bacterial genomes contain prophage-like structures, yet little effort has been made to use this information to determine the functions of these elements. The recent genomic sequencing of the marine bacterium Silicibacter sp. strain TM1040 revealed five prophage-like elements in its genome. The genomes of these prophages (named prophages 1 to 5) are approximately 74, 30, 39, 36, and 15 kb long, respectively. To understand the function of these prophages, cultures of TM1040 were treated with mitomycin C to induce the production of viral particles. A significant increase in viral counts and a decrease in bacterial counts when treated with mitomycin C suggested that prophages were induced from TM1040. Transmission electron microscopy revealed one dominant type of siphovirus, while pulsed-field gel electrophoresis demonstrated two major DNA bands, equivalent to 35 and 75 kb, in the lysate. PCR amplification with primer sets specific to each prophage detected the presence of prophages 1, 3, and 4 in the viral lysate, suggesting that these prophages are inducible, but not necessarily to the same level, while prophages 2 and 5 are likely defective or non-mitomycin C-inducible phages. The combination of traditional phage assays and modern microbial genomics provides a quick and efficient way to investigate the functions and inducibility of prophages, particularly for a host harboring multiple prophages with similar sizes and morphological features.

Auger Electron Spectroscopy and Its Application to Nanotechnology

2011 ◽  
Vol 19 (2) ◽  
pp. 12-15 ◽  
Author(s):  
S. N. Raman ◽  
D. F. Paul ◽  
J. S. Hammond ◽  
K. D. Bomben
Keyword(s):  
Electron Microscopy ◽  
Auger Electron Spectroscopy ◽  
Electron Spectroscopy ◽  
Auger Electron ◽  
Imaging Techniques ◽  
Chemical Characterization ◽  
Depth Resolution ◽  
Surface Modifications ◽  
Transmission Electron ◽  
Nanoscale Characterization

Over the past decade, the field of nanotechnology has expanded, and the most heavily used nanoscale characterization/imaging techniques have been scanning probe microscopy (SPM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Although these high-resolution imaging techniques help visualize nanostructures, it is essential to understand the chemical nature of these materials and their growth mechanisms. Surface modifications in the first few nanometers can alter the bulk properties of these nanostructures, and conventional characterization techniques, including energy dispersive spectroscopy (EDS) and electron energy loss spectroscopy (EELS) associated with SEM and TEM are not suited to detecting these surface modifications except in special, favorable specimens. A modern state-of-the-art scanning Auger electron spectroscopy (AES) instrument provides valuable elemental and chemical characterization of nanostructures with a lateral spatial resolution better than 10 nm and a depth resolution of a few nm. In this article we review the technique of scanning AES and highlight its unique analytical capabilities in the areas of nanotechnology, metallurgy, and semiconductors.

Hepatitis B virus: from immunobiology to immunotherapy

2012 ◽  
Vol 124 (2) ◽  
pp. 77-85 ◽  
Author(s):  
Daniel Grimm ◽  
Maximilian Heeg ◽  
Robert Thimme
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Therapeutic Approaches ◽  
Major Health ◽  
Antiviral Therapies ◽  
Adaptive Immune ◽  
Host Interaction ◽  
Current State ◽  
B Virus ◽  
Chronic Hbv

Owing to the major limitations of current antiviral therapies in HBV (hepatitis B virus) infection, there is a strong need for novel therapeutic approaches to this major health burden. Stimulation of the host's innate and adaptive immune responses in a way that results in the resolution of viral infection is a promising approach. A better understanding of the virus–host interaction in acute and chronic HBV infection revealed several possible novel targets for antiviral immunotherapy. In the present review, we will discuss the current state of the art in HBV immunology and illustrate how control of infection could be achieved by immunotherapeutic interventions.

Are there Viruses in Industrial Bioleaching Econiches?

2017 ◽  
Vol 262 ◽  
pp. 521-525 ◽  
Author(s):  
Paulo C. Covarrubias ◽  
Rodrigo Muñoz ◽  
Roberto A. Bobadilla-Fazzini ◽  
Patricio Martinez ◽  
Raquel Quatrini
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Microbial Ecology ◽  
Mineral Processing ◽  
Microbial Consortia ◽  
Basic Question ◽  
Host Interactions ◽  
Transmission Electron ◽  
Viral Particles ◽  
Stability Issues

Detailed descriptions of the consortia present in commercial mineral processing operations have emerged in recent years, improving our understanding of the biology and the ecology of bioleaching. In spite of this progress, one of the aspects of biomining microbial ecology that remains un-tackled is that of virus-host interactions. The effects of viruses on the dynamics of the bioleaching microbial consortia and their impact in metal recovery is presently unknown. To begin addressing this issue we asked a basic question: ¿Are there viruses in industrial bioleaching econiches? In this work, we answer that question experimentally, assessing the number and types of viral particles recovered in the leachates from different industrial settings, using epifluorescence and transmission electron microscopy. Findings emerging from this work point to an almost null presence of viral particles in the leachates from mineral processing operations, possibly due to structural stability issues of the particles in the extreme acidic and highly oxidant conditions favoured by their potential microbial hosts. In turn, DNA-loaded viral-size vesicles of presently unknown function are frequent and abundant in all samples analysed.

Sign in / Sign up

Export Citation Format

Share Document