Structure of ribosomes from a thermophilic bacterium

1989 ◽  
Vol 47 ◽  
pp. 1026-1027
Author(s):  
Janet Dickie ◽  
Karen Kyle ◽  
Derrick Flannigan ◽  
George Harauz
Keyword(s):  
Hot Springs ◽  
Thermophilic Bacteria ◽  
Structural Information ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Thermophilic Bacterium ◽  
Single Particles ◽  
Multivariate Statistical ◽  
Ribosomal Subunits ◽  
Dimensional Reconstruction

The most direct and informative probe of ribosome structure is electron microscopy (EM), of negatively stained and antibody-labelled specimens. Ribosomes from Escherichia coli have been the most intensively studied, although those from other prokaryotes and eukaryotes have also been imaged [e.g., 3, 4, 5],The amount of structural information obtained from electron images can be significantly increased using multivariate statistical analysis and classification techniques [e.g., 6]. Noisy electron micrographs of single particles are sorted according to their principal features, and average images formed with an enhanced signal-to-noise ratio and better reproducible resolution. The class averages represent projections from which a three-dimensional reconstruction can be computed.Thermus aguaticus is a species of extremely thermophilic bacteria isolated from environments such as hot springs. This species possesses macromolecular enzyme complexes with a great thermostability which must be reflected somehow instructural differences. In this study, we investigate the structures of ribosomes and ribosomal subunits from this bacterium.

Angular Calibration of Ribosomal Subuntts in Factor Space

1990 ◽  
Vol 48 (1) ◽  
pp. 462-463
Author(s):  
Minakhi Pujari ◽  
Joachim Frank
Keyword(s):  
Three Dimensional ◽  
Carbon Layer ◽  
Uranyl Acetate ◽  
Particle Analysis ◽  
Factor Space ◽  
Multivariate Statistical ◽  
Ribosomal Subunits ◽  
Layer Method ◽  
Dimensional Reconstruction ◽  
Number Of Particles

In single-particle analysis of macromolecule images with the electron microscope, variations of projections are often observed that can be attributed to the changes of the particle’s orientation on the specimen grid (“rocking”). In the multivariate statistical analysis (MSA) of such projections, a single factor is often found that expresses a large portion of these variations. Successful angle calibration of this “rocking factor” would mean that correct angles can be assigned to a large number of particles, thus facilitating three-dimensional reconstruction.In a study to explore angle calibration in factor space, we used 40S ribosomal subunits, which are known to rock around an axis approximately coincident with their long axis. We analyzed micrographs of a field of these particles, taken with 20° tilt and without tilt, using the standard methods of alignment and MSA. The specimen was prepared with the double carbon-layer method, using uranyl acetate for negative staining. In the MSA analysis, the untilted-particle projections were used as active, the tilted-particle projections as inactive objects. Upon tilting, those particles whose rocking axes are parallel to the tilt axis will change their appearance in the same way as under the influence of rocking. Therefore, each vector, in factor space, joining a tilted and untilted projection of the same particle can be regarded as a local 20-degree calibration bar.

scholarly journals Application of Symmetry Adapted Function Method for Three-Dimensional Reconstruction of Octahedral Biological Macromolecules

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Songjun Zeng ◽  
Hongrong Liu ◽  
Qibin Yang
Keyword(s):  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
Single Particles ◽  
Dimensional Reconstruction ◽  
Standard Models ◽  
Relative Errors ◽  
High Level ◽  
Influence Of Noise ◽  
Good Agreement

A method for three-dimensional (3D) reconstruction of macromolecule assembles, that is, octahedral symmetrical adapted functions (OSAFs) method, was introduced in this paper and a series of formulations for reconstruction by OSAF method were derived. To verify the feasibility and advantages of the method, two octahedral symmetrical macromolecules, that is, heat shock proteinDegp24and the Red-cell L Ferritin, were utilized as examples to implement reconstruction by the OSAF method. The schedule for simulation was designed as follows: 2000 random orientated projections of single particles with predefined Euler angles and centers of origins were generated, then different levels of noises that is signal-to-noise ratio (S/N)=0.1,0.5, and 0.8 were added. The structures reconstructed by the OSAF method were in good agreement with the standard models and the relative errors of the structures reconstructed by the OSAF method to standard structures were very little even for high level noise. The facts mentioned above account for that the OSAF method is feasible and efficient approach to reconstruct structures of macromolecules and have ability to suppress the influence of noise.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

Computer Assisted Image Reconstruction of Oligomer Structure

1976 ◽  
Vol 34 ◽  
pp. 472-473
Author(s):  
A.M. Jones ◽  
A. Max Fiskin
Keyword(s):  
Three Dimensional ◽  
Depth Of Field ◽  
Computer Assisted ◽  
Projection Data ◽  
Two Dimensional ◽  
Single Particles ◽  
Dimensional Reconstruction ◽  
Computer Assisted Image ◽  
The Fourier Transform ◽  
Space Approach

If the tilt of a specimen can be varied either by the strategy of observing identical particles orientated randomly or by use of a eucentric goniometer stage, three dimensional reconstruction procedures are available (l). If the specimens, such as small protein aggregates, lack periodicity, direct space methods compete favorably in ease of implementation with reconstruction by the Fourier (transform) space approach (2). Regardless of method, reconstruction is possible because useful specimen thicknesses are always much less than the depth of field in an electron microscope. Thus electron images record the amount of stain in columns of the object normal to the recording plates. For single particles, practical considerations dictate that the specimen be tilted precisely about a single axis. In so doing a reconstructed image is achieved serially from two-dimensional sections which in turn are generated by a series of back-to-front lines of projection data.

Three-dimensional reconstruction of the 40S ribosomal subunit from rabbit reticulocytes

1987 ◽  
Vol 45 ◽  
pp. 936-937
Author(s):  
Neng-Yu Zhang ◽  
Terence Wagenknecht ◽  
Michael Radermacher ◽  
Tom Obrig ◽  
Joachim Frank
Keyword(s):  
Three Dimensional ◽  
Ribosomal Subunit ◽  
Uranyl Acetate ◽  
Reconstruction Method ◽  
Single Exposure ◽  
Electron Dose ◽  
Ribosomal Subunits ◽  
40S Ribosomal Subunit ◽  
Dimensional Reconstruction ◽  
Rabbit Reticulocytes

We have reconstructed the 40S ribosomal subunit at a resolution of 4 nm using the single-exposure pseudo-conical reconstruction method of Radermacher et al.Small (40S) ribosomal subunits were Isolated from rabbit reticulocytes, applied to grids and negatively stained (0.5% uranyl acetate) in a manner that “sandwiches” the specimen between two layers of carbon. Regions of the grid exhibiting uniform and thick staining were identified and photographed twice (magnification 49,000X). The first micrograph was always taken with the specimen tilted by 50° and the second was of the Identical area untilted (Fig. 1). For each of the micrographs the specimen was subjected to an electron dose of 2000-3000 el/nm2.Three hundred thirty particles appearing in the L view (defined in [4]) were selected from both tilted- and untilted-specimen micrographs. The untilted particles were aligned and their rotational alignment produced the azimuthal angles of the tilted particles in the conical tilt series.

Denoising and 3D Reconstruction of CT Images in Extracted Tooth via Wavelet and Bilateral Filtering

2018 ◽  
Vol 32 (05) ◽  
pp. 1854010 ◽  
Author(s):  
Cuizhen Wang ◽  
Zhenxue Chen ◽  
Yan Wang ◽  
Zhifeng Wang
Keyword(s):  
3D Reconstruction ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Similarity Index ◽  
Low Frequency ◽  
Structural Similarity ◽  
Bilateral Filtering ◽  
Denoising Method ◽  
Dimensional Reconstruction ◽  
Index Measure

Three-dimensional reconstruction of teeth plays an important role in the operation of living dental implants. However, the tissue around teeth and the noise generated in the process of image acquisition bring a serious impact on the reconstruction results, which must be reduced or eliminated. Combined with the advantages of wavelet transform and bilateral filtering, this paper proposes an image denoising method based on the above methods. The method proposed in this paper not only removes the noise but also preserves the image edge details. The noise in high frequency subbands is denoised using a locally adaptive thresholding and the noise in low frequency subbands is filtered by the bilateral filtering. Peak signal-to-noise ratio (PSNR), structural similarity index measure (SSIM) and 3D reconstruction using the iso-surface extraction method are used to evaluate the denoising effect. The experimental results show that the proposed method is better than the wavelet denoising and bilateral filtering, and the reconstruction results meet the requirements of clinical diagnosis.

Anoxybacillus sp. AH1, an α-amylase-producing thermophilic bacterium isolated from Dargeçit hot spring

Biologia ◽  
2015 ◽  
Vol 70 (7) ◽  
Author(s):  
Ömer Acer ◽  
Hemşe Pırınççiğlu ◽  
Fatma Matpan Bekler ◽  
Reyhan Gül-Güven
Keyword(s):  
Hot Springs ◽  
Hot Spring ◽  
Thermophilic Bacteria ◽  
Potato Starch ◽  
Nitrogen Sources ◽  
Soluble Starch ◽  
Thermophilic Bacterium ◽  
Carbon And Nitrogen Sources ◽  
Carbon And Nitrogen ◽  
Optimum Growth Temperature

AbstractThe present study was conducted to isolate α-amylase-producing thermophilic bacteria from Darge¸cit hot springs in Turkey. The morphological, biochemical and physiological characterisation, as well as genetic analysis by 16S rRNA sequences indicated that the isolated strain AH1 was a member of Anoxybacillus genus. The strain was aerobe, Gram-positive and spore-forming rod, exhibiting optimum growth temperature and pH of 60ºC and 7.0-7.5, respectively. Optimization of growth medium and enzyme assay conditions for extracellular α-amylase production by the novel thermophilic Anoxybacillus sp. AH1 were carried out in many different media containing a variety of carbon and nitrogen sources. Among various carbon and nitrogen sources, peptone (2054.1 U/mL) at 1% and maltose (1862.9 U/mL) at 0.5% increased α-amylase activity, compared to controls. Moreover, a high enzyme production was observed with potato starch at 0.5% and 1% (2668.4 U/mL and 3627 U/mL, respectively), as well as with 1% soluble starch (2051.9 U/mL). The enzyme activity was found to be rather high in the presence of CaCl

Challenges of three-dimensional reconstruction of ribonucleoprotein complexes from electron spectroscopic images - Reconstructing ribosomal RNA

1996 ◽  
Vol 54 ◽  
pp. 52-53
Author(s):  
D.R. Beniac ◽  
G.J. Czarnota ◽  
T.A. Bartlett ◽  
F.P. Ottensmeyer ◽  
G. Harauz
Keyword(s):  
Ribosomal Rna ◽  
Correlation Functions ◽  
Three Dimensional ◽  
Three Dimensional Reconstruction ◽  
Mutual Correlation ◽  
Ribosomal Subunits ◽  
E Coli ◽  
Ribonucleoprotein Complexes ◽  
Dimensional Reconstruction

Transmission electron microscopy has been dominant in structural studies of the ribosome and its constituent ribonucleic acids and proteins. Ribosomal RNA (rRNA) has central importance in the architecture of this complex and in protein synthesis. Our work has entailed using electron spectroscopic imaging (ESI) to probe the tertiary structure of rRNA in situ in a prokaryote (Escherichia coli) and in a eukaryote (Thermomyces lanuginosus). ESI uses only electrons which have lost a specific amount of energy due to specific inner-shell ionisation interactions with the specimen to form an elemental map. In nucleoprotein complexes, a map of the phosphorus distribution represents primarily a projection of the phosphate backbone of the nucleic acid component. The visualisation of rRNA in situ in the intact ribosomal subunit by ESI was demonstrated almost a decade ago to be feasible. Our work on quantitative image analysis of ES images of E. coli and Th. lanuginosus ribosomal subunits has presented unique challenges and has resulted in new algorithmic developments generally applicable to such images. These innovations include a singular pretreatment procedure, the use of mutual correlation functions rather than cross correlation functions to reduce the effect of low spatial frequency components, and angular determination using iterative quaternion-assisted angular reconstitution to compute a three-dimensional reconstruction. These investigations have produced direct information regarding ribosomal rRNA localisation in the ribosomal subunits of E. coli and Th. lanuginosus, and the position of non-conserved sequences.

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