scholarly journals Crystal Structure of a 9-Subunit Archaeal Exosome in Pre-Catalytic States of the Phosphorolytic Reaction

Archaea ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Esben Lorentzen ◽  
Elena Conti
Keyword(s):  
Accurate Determination ◽  
Nucleophilic Attack ◽  
Divalent Metal Ions ◽  
Mechanism Of Catalysis ◽  
Rna Exosome ◽  
Eukaryotic Organisms ◽  
High Degree ◽  
Shed Light ◽  
Positively Charged

The RNA exosome is an important protein complex that functions in the 3′ processing and degradation of RNA in archaeal and eukaryotic organisms. The archaeal exosome is functionally similar to bacterial polynucleotide phosphorylase (PNPase) and RNase PH enzymes as it uses inorganic phosphate (Pi) to processively cleave RNA substrates releasing nucleoside diphosphates. To shed light on the mechanism of catalysis, we have determined the crystal structures of mutant archaeal exosome in complex with either Pi or with both RNA and Pi at resolutions of 1.8 Å and 2.5 Å, respectively. These structures represent views of precatalytic states of the enzyme and allow the accurate determination of the substrate binding geometries. In the structure with both Pi and RNA bound, the Pi closely approaches the phosphate of the 3′-end nucleotide of the RNA and is in a perfect position to perform a nucleophilic attack. The presence of negative charge resulting from the close contacts between the phosphates appears to be neutralized by conserved positively charged residues in the active site of the archaeal exosome. The high degree of structural conservation between the archaeal exosome and the PNPase including the requirement for divalent metal ions for catalysis is discussed.

scholarly journals Porous or non-porous? The challenge of studying unusual placoid sensilla of Megaphragma wasps (Hymenoptera, Trichogrammatidae) with electron microscopy

2021 ◽  
Vol 84 ◽  
pp. 69-73
Author(s):  
Anna V. Diakova ◽  
Alexey A. Polilov
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Accurate Determination ◽  
Apparent Absence ◽  
Olfactory Sensilla ◽  
High Degree ◽  
Scanning Electron

Extreme miniaturization implies a high degree of optimization, rendering the retention of non-functional organs almost impossible. Two unique non-porous placoid sensilla on the antennae of females of Megaphragma were described in the literature. Placoid sensilla in Hymenoptera have an olfactory function and always bear pores; the apparent absence of pores therefore raises the questions whether such sensilla are functional in Megaphragma and whether their surface sculpture had been sufficiently well examined. We examined in detail the external microsculpture and internal ultrastructure of the placoid sensilla using Focused Ion Beam Scanning Electron Microscopy and Scanning Electron Microscopy with various types of sputtering and show that these sensilla actually have a porous cuticle and are innervated by 11 or 12 neurons with branched cilia, which is typical of olfactory sensilla. Comparison of various methods of electron microscopy allows us to conclude that for an accurate determination of the morphofunctional types of sensilla, especially in miniature insects, it is necessary to study both the internal ultrastructure of the sensilla and their external morphology using carefully selected scanning electron microscopy methods.

A principle for counting tissue structures on random sections

1962 ◽  
Vol 17 (2) ◽  
pp. 343-348 ◽  
Author(s):  
Ewald R. Weibel ◽  
Domingo M. Gomez
Keyword(s):  
Unit Volume ◽  
Unit Area ◽  
Accurate Determination ◽  
Volumetric Density ◽  
Human Lungs ◽  
Random Sections ◽  
Normal Human ◽  
High Degree ◽  
Random Section

A new principle is derived from mathematical considerations which will allow the calculation of the number of bodies contained in the unit volume by counting the number of transections on the unit area of a random section. The simple equation involves two coefficients related to the volumetric density of the bodies in the volume, and to their configuration. Means for the accurate determination of these coefficients are given. The verification of this principle in model experiments showed a high degree of reliability of the method with average errors of estimate of 2–4%. The method has been applied to the counting of alveoli in five normal human lungs, which were found to number an average of 300 million, with a striking constancy from lung to lung. Submitted on May 31, 1961

scholarly journals Extensive Testing and Comparison of a New Type of Target for Use in Engineering Surveying

2013 ◽  
Vol 21 (2) ◽  
pp. 29-40
Author(s):  
Jaroslav Braun ◽  
Martin Štroner ◽  
Rudolf Urban
Keyword(s):  
Accurate Determination ◽  
Steel Structures ◽  
Engineering Structures ◽  
Steel Construction ◽  
Spatial Coordinates ◽  
New Type ◽  
Correct Angle ◽  
High Degree ◽  
Reflective Foil

Abstract The paper deals with the testing of a special target for determining the exact dimensions of steel structures and their descriptions. In most cases, the accuracy required in mechanical engineering is on the order of millimetres, and the location of a point on a steel construction is marked by a centre punch. Due to the segmentation of steel constructions and the impossibility of the vertical placement of a target, it is very difficult to use ordinary prisms because of their size and the linear error from a wrong rotation and a nontrivial conversion of the centre of a prism into a centre punch on a steel construction. For a more accurate determination of spatial coordinates, a special reflective target with a reflective foil and a mechanical collimator, which ensures the correct angle to the target device according to the instructions of the person at the instrument, has been developed. Centration with a high degree of accuracy is achieved by a spike. Its functionality and usability goals have been tested and compared with standard methods of measurements and goals in engineering structures.

A quantitative approach to inner shell losses

1978 ◽  
Vol 36 (1) ◽  
pp. 526-527 ◽  
Author(s):  
R.D. Leapman ◽  
P. Rez ◽  
D.F. Mayers
Keyword(s):  
Energy Transfer ◽  
Cross Section ◽  
Cross Sections ◽  
Accurate Determination ◽  
Background Intensity ◽  
Core Excitation ◽  
Quantitative Basis ◽  
Cross Section Differential ◽  
Bound Electrons

Microanalysis by EELS has been developing rapidly and though the general form of the spectrum is now understood there is a need to put the technique on a more quantitative basis (1,2). Certain aspects important for microanalysis include: (i) accurate determination of the partial cross sections, σx(α,ΔE) for core excitation when scattering lies inside collection angle a and energy range ΔE above the edge, (ii) behavior of the background intensity due to excitation of less strongly bound electrons, necessary for extrapolation beneath the signal of interest, (iii) departures from the simple hydrogenic K-edge seen in L and M losses, effecting σx and complicating microanalysis. Such problems might be approached empirically but here we describe how computation can elucidate the spectrum shape.The inelastic cross section differential with respect to energy transfer E and momentum transfer q for electrons of energy E0 and velocity v can be written as

Feasibility of Molecular Structure Determination With a High Resolution Electron Microscope

1968 ◽  
Vol 26 ◽  
pp. 338-339
Author(s):  
T. A. Welton
Keyword(s):  
Electron Microscope ◽  
Substrate Surface ◽  
Helical Axis ◽  
Base Plane ◽  
Resolution Electron ◽  
High Resolution Electron Microscope ◽  
High Degree ◽  
Degree Of Order ◽  
Purine Pyrimidine

An ultimate design goal for an improved electron microscope, aimed at biological applications, is the determination of the structure of complex bio-molecules. As a prototype of this class of problems, we propose to examine the possibility of reading DNA sequence by an imaginable instrument design. This problem ideally combines absolute importance and relative simplicity, in as much as the problem of enzyme structure seems to be a much more difficult one.The proposed technique involves the deposition on a thin graphite lamina of intact double helical DNA rods. If the structure can be maintained under vacuum conditions, we can then make use of the high degree of order to greatly reduce the work involved in discriminating between the four possible purine-pyrimidine arrangements in each base plane. The phosphorus atoms of the back bone form in projection (the helical axis being necessarily parallel to the substrate surface) two intertwined sinusoids. If these phosphorus atoms have been located up to a certain point on the molecule, we have available excellent information on the orientation of the base plane at that point, and can then locate in projection the key atoms for discrimination of the four alternatives.

Fast calibration of CBED patterns for quantitative analysis

1993 ◽  
Vol 51 ◽  
pp. 674-675
Author(s):  
M.A. Gribelyuk ◽  
M. Rühle
Keyword(s):  
Reciprocal Lattice ◽  
Accurate Determination ◽  
Incident Beam ◽  
Crystal Thickness ◽  
Structure Model ◽  
Beam Direction ◽  
Transmitted Beam ◽  
Reciprocal Vector ◽  
On Line

A new method is suggested for the accurate determination of the incident beam direction K, crystal thickness t and the coordinates of the basic reciprocal lattice vectors V1 and V2 (Fig. 1) of the ZOLZ plans in pixels of the digitized 2-D CBED pattern. For a given structure model and some estimated values Vest and Kest of some point O in the CBED pattern a set of line scans AkBk is chosen so that all the scans are located within CBED disks.The points on line scans AkBk are conjugate to those on A0B0 since they are shifted by the reciprocal vector gk with respect to each other. As many conjugate scans are considered as CBED disks fall into the energy filtered region of the experimental pattern. Electron intensities of the transmitted beam I0 and diffracted beams Igk for all points on conjugate scans are found as a function of crystal thickness t on the basis of the full dynamical calculation.

Computer-Assisted High-Re Solution TEM

1990 ◽  
Vol 48 (1) ◽  
pp. 162-163
Author(s):  
F.A. Ponce ◽  
H. Hikashi
Keyword(s):  
Signal To Noise Ratio ◽  
Accurate Determination ◽  
Computer Software ◽  
Video Camera ◽  
Image Contrast ◽  
Objective Lens ◽  
Computer Assisted ◽  
Optical Parameters ◽  
Astigmatism Correction

The determination of the atomic positions from HRTEM micrographs is only possible if the optical parameters are known to a certain accuracy, and reliable through-focus series are available to match the experimental images with calculated images of possible atomic models. The main limitation in interpreting images at the atomic level is the knowledge of the optical parameters such as beam alignment, astigmatism correction and defocus value. Under ordinary conditions, the uncertainty in these values is sufficiently large to prevent the accurate determination of the atomic positions. Therefore, in order to achieve the resolution power of the microscope (under 0.2nm) it is necessary to take extraordinary measures. The use of on line computers has been proposed [e.g.: 2-5] and used with certain amount of success.We have built a system that can perform operations in the range of one frame stored and analyzed per second. A schematic diagram of the system is shown in figure 1. A JEOL 4000EX microscope equipped with an external computer interface is directly linked to a SUN-3 computer. All electrical parameters in the microscope can be changed via this interface by the use of a set of commands. The image is received from a video camera. A commercial image processor improves the signal-to-noise ratio by recursively averaging with a time constant, usually set at 0.25 sec. The computer software is based on a multi-window system and is entirely mouse-driven. All operations can be performed by clicking the mouse on the appropiate windows and buttons. This capability leads to extreme friendliness, ease of operation, and high operator speeds. Image analysis can be done in various ways. Here, we have measured the image contrast and used it to optimize certain parameters. The system is designed to have instant access to: (a) x- and y- alignment coils, (b) x- and y- astigmatism correction coils, and (c) objective lens current. The algorithm is shown in figure 2. Figure 3 shows an example taken from a thin CdTe crystal. The image contrast is displayed for changing objective lens current (defocus value). The display is calibrated in angstroms. Images are stored on the disk and are accessible by clicking the data points in the graph. Some of the frame-store images are displayed in Fig. 4.

Turkish policy towards Libya after the February 2011 revolution

2020 ◽  
pp. 31
Author(s):  
Rafea Shareef Dhanoon
Keyword(s):  
International Law ◽  
Military Cooperation ◽  
The West ◽  
Regional Parties ◽  
Spheres Of Influence ◽  
Close Relationship ◽  
Shed Light

The close relations between Turkey and Libya are still on the rise, and this was evident through Turkish support at all levels of the internationally recognized government of Al-Sarraj winner. The Memorandum of Understanding signed between Turkey and Libya on 27 / November 2019, in the areas of security and military cooperation and the determination of areas of influence revealed The navy, the extent of the historical close relationship between Ankara and Tripoli, just as the Turkish President Erdogan wanted to deliver a message to the West and other regional parties after the signing of the Memorandum of Understanding, that Turkey has a non-negotiable sovereign right to define the maritime spheres of influence and that this right stems from international law. In light of these tracks, we will shed light on the orientations of Turkish policy towards Libya after the February 2011 revolution, by defining the determinants of those trends and examining the most important obstacles in the march of Turkish policy towards Libya.

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