scholarly journals Characterization of SARS-CoV-2 East Java isolate, Indonesia

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 480
Author(s):  
Fedik Abdul Rantam ◽  
Cita Rosita Sigit Prakoeswa ◽  
Damayanti Tinduh ◽  
Jusak Nugraha ◽  
Helen Susilowati ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
High Titer ◽  
Rabbit Serum ◽  
Good Growth ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Chain Reactions ◽  
Spike Gene ◽  
Three Samples ◽  
Scanning Transmission

Background: Incidents of SARS-CoV-2 in East Java increased steadily, and it became the second epicenter in Indonesia. The COVID-19 pandemic caused a dire multisectoral crisis all around the world. This study investigates and characterizes local isolates from East Java, Indonesia.   Methods: There were 54 patients suspected with SARS-COV-2 infection and 27 patients were COVID-19 positive. Virus isolates were obtained from COVID-19 inpatients’ nasopharyngeal swabs at the Dr Soetomo Teaching Hospital, Surabaya. There were only three isolates (#6, #11, #35) with good growth characteristics. Serial blind passage and cytopathic effect observation in the Vero E6 cell line were performed for virus isolation. Confirmation of the SARS-CoV-2 infection was proven by means of reverse transcriptase-polymerase chain reactions using SARS-CoV-2 specific primers, scanning electron microscopy, and scanning transmission electron microscopy examination. Whole genome sequencing was performed using ARTIC protocol. Furthermore, SARS-CoV-2 characterization was identified through a western blot using rabbit serum immunized with inactive SARS-CoV-2 vaccine and human natural COVID-19 infection serum.   Results: Spike gene analysis of three samples (#6, #11, #35) found that the D614G mutation was detected in all isolates, although one isolate exhibited the D215Y and E484D mutation. Based on whole genome analysis, those three isolates were included in clade 20A, and two isolates were included in lineage B.1.6 with one isolate belongs to lineage B.1.4.7.   Conclusion: Based on molecular characterization and immunogenicity of SARS-CoV-2 East Java, Indonesia showed high titer and it has mutation in some regions.

scholarly journals Electron microscopic observation of infected CCB and whole genome analysis of Koi herpesvirus isolate GY01

2020 ◽  
Author(s):  
Hongan Duan ◽  
Ye Xu ◽  
Yi Zhou ◽  
Fengzhi Wang ◽  
Chao Ding ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Phylogenetic Analysis ◽  
Genome Analysis ◽  
Multiple Alignment ◽  
Whole Genome ◽  
Electron Microscopic ◽  
Whole Genome Analysis ◽  
Koi Herpesvirus ◽  
Whole Genomes ◽  
Microscopy Examination

AbstractBackgroundCyprinid herpesvirus- 3 (CyHV-3), commonly known as Koi herpesvirus (KHV) can induce infectious and acute viremia in common/koi carp (Cyprinus carpio). In an earlier study in this laboratory a KHV isolate GY1506 (KHV GY01 in GeneBank) was isolated from diseased common carp, replicated on CCB cells and identified by PCR targeted on and phylogenetic analysis of thymidine kinase (TK) gene. Electron microscopy examination of GY01 infected CCB cell line and whole genome analysis was studied for further characteristics and epidemiological features of this strain.ResultsElectron microscopy examination of CCB infected with KHV GY01 strain revealed destruct of infected cells including incomplete nuclear membranes, deformed nucleus, marginalized nuclear chromosome, and the virus of different development stages and morphologies in the cytoplasm and nucleus, which resembles the herpesvirus. MEGA X and phyML were used for multiple alignment and phylogenetic analysis of whole genomes of GY01 and other 21 KHV strains available in GeneBank. analysis showed that GY01 was more close to E and KHV-I and was predicted it originated from the same ancestor as the E and KHV-I. Pairwise alignment of strain GY01 and strain E by Geneious software and YASS online version revealed that two strains had high identity(99.1%) at the nucleotide sequence level although variations and disagreement existed. The number and structure arrangement of open reading frames (orfs) or protein-encoding genes of GY01 is very similar to KHV E, and also to KHV-U but different from KHV-I. The characteristics and function of each orf need further study in the future.ConclusionsPathogenic changes of infected CCB cells and morphologies of KHV GY01 resembles the herpesvirus. Pairwise, multiple alignment and phylogenetic analysis of whole genomes of GY01 and other 21 KHV strains available in GeneBank demonstrated that the GY01 is closely related to strain KHV E and KHV-I and suggested it originated from the same ancestor as the E and KHV-I.

High-Voltage Scanning Electron Microscopy

1970 ◽  
Vol 28 ◽  
pp. 6-7
Author(s):  
J. M. Cowley
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Scanning Transmission Electron Microscopy ◽  
Wave Optics ◽  
Contrast Effects ◽  
Transmission Electron ◽  
Mode Of Operation ◽  
Scanning Transmission ◽  
Types Of Information ◽  
Voltage Scanning

The comparison of scanning transmission electron microscopy (STEM) with conventional transmission electron microscopy (CTEM) can best be made by means of the Reciprocity Theorem of wave optics. In Fig. 1 the intensity measured at a point A’ in the CTEM image due to emission from a point B’ in the electron source is equated to the intensity at a point of the detector, B, due to emission from a point A In the source In the STEM. On this basis it can be demonstrated that contrast effects In the two types of instrument will be similar. The reciprocity relationship can be carried further to include the Instrument design and experimental procedures required to obtain particular types of information. For any. mode of operation providing particular information with one type of microscope, the analagous type of operation giving the same information can be postulated for the other type of microscope. Then the choice between the two types of instrument depends on the practical convenience for obtaining the required Information.

Development of 200 kV Scanning-Transmission Electron Microscope

1974 ◽  
Vol 32 ◽  
pp. 410-411
Author(s):  
H. Koike ◽  
S. Sakurai ◽  
K. Ueno ◽  
M. Watanabe
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Scanning Transmission Electron Microscope ◽  
The Other ◽  
Morphological Observation ◽  
Magnetic Domains ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Backscattered Electron ◽  
Increasing Demand

In recent years, there has been increasing demand for higher voltage SEMs, in the field of surface observation, especially that of magnetic domains, dislocations, and electron channeling patterns by backscattered electron microscopy. On the other hand, the resolution of the CTEM has now reached 1 ∼ 2Å, and several reports have recently been made on the observation of atom images, indicating that the ultimate goal of morphological observation has beem nearly achieved.

High-resolution x-ray imaging of small copper-rich precipitates in steels

1988 ◽  
Vol 46 ◽  
pp. 528-529
Author(s):  
J. R. Michael ◽  
K. A. Taylor
Keyword(s):  
Electron Microscopy ◽  
Thermomechanical Processing ◽  
Atom Probe ◽  
Ferrite Matrix ◽  
Scanning Transmission Electron Microscope ◽  
Probe Field ◽  
X Ray ◽  
Subsequent Transformation ◽  
Transmission Electron ◽  
Scanning Transmission

Although copper is considered an incidental or trace element in many commercial steels, some grades contain up to 1-2 wt.% Cu for precipitation strengthening. Previous electron microscopy and atom-probe/field-ion microscopy (AP/FIM) studies indicate that the precipitation of copper from ferrite proceeds with the formation of Cu-rich bcc zones and the subsequent transformation of these zones to fcc copper particles. However, the similarity between the atomic scattering amplitudes for iron and copper and the small misfit between between Cu-rich particles and the ferrite matrix preclude the detection of small (<5 nm) Cu-rich particles by conventional transmission electron microscopy; such particles have been imaged directly only by FIM. Here results are presented whereby the Cu Kα x-ray signal was used in a dedicated scanning transmission electron microscope (STEM) to image small Cu-rich particles in a steel. The capability to detect these small particles is expected to be helpful in understanding the behavior of copper in steels during thermomechanical processing and heat treatment.

Application of analytical electron microscopy to studies of equilibrium and non-equilibrium segregation in materials

1992 ◽  
Vol 50 (2) ◽  
pp. 1214-1215
Author(s):  
Edward A Kenik
Keyword(s):  
Electron Microscopy ◽  
Analytical Electron Microscopy ◽  
Extended Defects ◽  
Probe Diameter ◽  
Specimen Holder ◽  
Analytical Electron ◽  
Scanning Transmission ◽  
Solute Atoms ◽  
Equilibrium Segregation ◽  
Non Equilibrium

Segregation of solute atoms to grain boundaries, dislocations, and other extended defects can occur under thermal equilibrium or non-equilibrium conditions, such as quenching, irradiation, or precipitation. Generally, equilibrium segregation is narrow (near monolayer coverage at planar defects), whereas non-equilibrium segregation exhibits profiles of larger spatial extent, associated with diffusion of point defects or solute atoms. Analytical electron microscopy provides tools both to measure the segregation and to characterize the defect at which the segregation occurs. This is especially true of instruments that can achieve fine (<2 nm width), high current probes and as such, provide high spatial resolution analysis and characterization capability. Analysis was performed in a Philips EM400T/FEG operated in the scanning transmission mode with a probe diameter of <2 nm (FWTM). The instrument is equipped with EDAX 9100/70 energy dispersive X-ray spectrometry (EDXS) and Gatan 666 parallel detection electron energy loss spectrometry (PEELS) systems. A double-tilt, liquid-nitrogen-cooled specimen holder was employed for microanalysis in order to minimize contamination under the focussed spot.

Magnesium and sulfur in mast cell and basophil granules of lower vertebrates in relation with histamine

1992 ◽  
Vol 50 (2) ◽  
pp. 1596-1597
Author(s):  
Kenichi Takaya
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Mast Cell ◽  
Mast Cells ◽  
Tree Frog ◽  
X Ray ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Fresh Frozen ◽  
Ultrathin Sections

Mast cell and basophil granules of the vertebrate contain heparin or related sulfated proteoglycans. Histamine is also present in mammalian mast cells and basophils. However, no histamine is detected in mast cell granules of the amphibian or fish, while it is shown in those of reptiles and birds A quantitative x-ray microanalysis of mast cell granules of fresh frozen dried ultrathin sections of the tongue of Wistar rats and tree frogs disclosed high concentrations of sulfur in rat mast cell granules and those of sulfur and magnesium in the tree frog granules. Their concentrations in tree frog mast cell granules were closely correlated (r=0.94).Fresh frozen dried ultrathin sections and fresh air-dried prints of the tree frog tongue and spleen and young red-eared turtle (ca. 6 g) spleen and heart blood were examined by a quantitative energy-dispersive x-ray microanalysis (X-650, Kevex-7000) for the element constituents of the granules of mast cells and basophils. The specimens were observed by transmission electron microscopy (TEM) (80-200 kV) and followed by scanning transmission electron microscopy (STEM) under an analytical electron microscope (X-650) at an acceleration voltage of 40 kV and a specimen current of 0.2 nA. A spot analysis was performed in a STEM mode for 100 s at a specimen current of 2 nA on the mast cell and basophil granules and other areas of the cells. Histamine was examined by the o-phthalaldehyde method.

The effect of small additions of Cu on precipitation in Al-Mg-Si alloys

1990 ◽  
Vol 48 (2) ◽  
pp. 442-443
Author(s):  
M. Tamizifar ◽  
G. Cliff ◽  
R.W. Devenish ◽  
G.W. Lorimer
Keyword(s):  
Electron Microscopy ◽  
Analytical Electron Microscopy ◽  
Scanning Transmission Electron Microscope ◽  
Argon Atmosphere ◽  
Age Hardening ◽  
X Ray ◽  
Transmission Electron ◽  
Heat Treated ◽  
Analytical Electron ◽  
Scanning Transmission

Small additions of copper, <1 wt%, have a pronounced effect on the ageing response of Al-Mg-Si alloys. The object of the present investigation was to study the effect of additions of copper up to 0.5 wt% on the ageing response of a series of Al-Mg-Si alloys and to use high resolution analytical electron microscopy to determine the composition of the age hardening precipitates.The composition of the alloys investigated is given in Table 1. The alloys were heat treated in an argon atmosphere for 30m, water quenched and immediately aged either at 180°C for 15 h or given a duplex treatment of 180°C for 15 h followed by 350°C for 2 h2. The double-ageing treatment was similar to that carried out by Dumolt et al. Analyses of the precipitation were carried out with a HB 501 Scanning Transmission Electron Microscope. X-ray peak integrals were converted into weight fractions using the ratio technique of Cliff and Lorimer.

Identification of Maize Rayado Fino Virus by Immunoelectron Microscopy

1985 ◽  
Vol 43 ◽  
pp. 636-637
Author(s):  
O. E. Bradfute
Keyword(s):  
Electron Microscopy ◽  
Zea Mays ◽  
Costa Rica ◽  
Severe Disease ◽  
Rabbit Serum ◽  
Normal Rabbit Serum ◽  
Virus Particles ◽  
Far North ◽  
Maize Rayado Fino Virus ◽  
Antibody Coating

Maize rayado fino virus (MRFV) causes a severe disease of corn (Zea mays) in many locations throughout the neotropics and as far north as southern U.S. MRFV particles detected by direct electron microscopy of negatively stained sap from infected leaves are not necessarily distinguishable from many other small isometric viruses infecting plants (Fig. 1).Immunosorbent trapping of virus particles on antibody-coated grids and the antibody coating or decoration of trapped virus particles, was used to confirm the identification of MRFV. Antiserum to MRFV was supplied by R. Gamez (Centro de Investigacion en Biologia Celular y Molecular, Universidad de Costa Rica, Ciudad Universitaria, Costa Rica).Virus particles, appearing as a continuous lawn, were trapped on grids coated with MRFV antiserum (Fig. 2-4). In contrast, virus particles were infrequently found on grids not exposed to antiserum or grids coated with normal rabbit serum (similar to Fig. 1). In Fig. 3, the appearance of the virus particles (isometric morphology, 30 nm diameter, stain penetration of some particles, and morphological subunits in other particles) is characteristic of negatively stained MRFV particles. Decoration or coating of these particles with MRFV antiserum confirms their identification as MRFV (Fig. 4).

Atomic resolution Z-contrast imaging of bulk crystal surfaces in Scanning Reflection Electron Microscopy

1990 ◽  
Vol 48 (4) ◽  
pp. 414-415
Author(s):  
Z. L. Wang ◽  
J. Bentley
Keyword(s):  
Electron Microscopy ◽  
Elastic Scattering ◽  
Dark Field ◽  
Contrast Imaging ◽  
Crystal Lattices ◽  
Small Probe ◽  
Scanning Transmission ◽  
Annular Dark Field ◽  
Image Position ◽  
Z Contrast

The success of obtaining atomic-number-sensitive (Z-contrast) images in scanning transmission electron microscopy (STEM) has shown the feasibility of imaging composition changes at the atomic level. This type of image is formed by collecting the electrons scattered through large angles when a small probe scans across the specimen. The image contrast is determined by two scattering processes. One is the high angle elastic scattering from the nuclear sites,where ϕNe is the electron probe function centered at bp = (Xp, yp) after penetrating through the crystal; F denotes a Fourier transform operation; D is the detection function of the annular-dark-field (ADF) detector in reciprocal space u. The other process is thermal diffuse scattering (TDS), which is more important than the elastic contribution for specimens thicker than about 10 nm, and thus dominates the Z-contrast image. The TDS is an average “elastic” scattering of the electrons from crystal lattices of different thermal vibrational configurations,

Electron Microscopy Studies of The Chemistry And Microstructure of BaF2 / YBa2Cu3O7-x Thin Films

1994 ◽  
Vol 52 ◽  
pp. 796-797
Author(s):  
J. L. Lee ◽  
C. A. Weiss ◽  
R. A. Buhrman ◽  
J. Silcox
Keyword(s):  
Thin Film ◽  
Electron Microscopy ◽  
Thin Films ◽  
Scanning Transmission Electron Microscope ◽  
Atomic Scale ◽  
Island Growth ◽  
Multilayer Systems ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Mgo Substrate

BaF2 thin films are being investigated as candidates for use in YBa2Cu3O7-x (YBCO) / BaF2 thin film multilayer systems, given the favorable dielectric properties of BaF2. In this study, the microstructural and chemical compatibility of BaF2 thin films with YBCO thin films is examined using transmission electron microscopy and microanalysis. The specimen was prepared by using laser ablation to first deposit an approximately 2500 Å thick (0 0 1) YBCO thin film onto a (0 0 1) MgO substrate. An approximately 7500 Å thick (0 0 1) BaF2 thin film was subsequendy thermally evaporated onto the YBCO film.Images from a VG HB501A UHV scanning transmission electron microscope (STEM) operating at 100 kV show that the thickness of the BaF2 film is rather uniform, with the BaF2/YBCO interface being quite flat. Relatively few intrinsic defects, such as hillocks and depressions, were evident in the BaF2 film. Moreover, the hillocks and depressions appear to be faceted along {111} planes, suggesting that the surface is smooth and well-ordered on an atomic scale and that an island growth mechanism is involved in the evolution of the BaF2 film.

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