Abstract OR-2: The Formation of Dps-DNA Complexes under Different Conditions According to Cryo-EM and SAXS

Background: The effect of Dps-DNA co-crystals formation, which occurs in stressed Escherichia coli cells exposed to extreme conditions, is well described in the literature. However, the exact mechanisms of co-crystals formation are yet to be postulated remaining largely unknown. Here we summarize the results obtained by our group over the last few years using cryo-Electron Microscopy (cryo-EM) and Small Angle X-ray Scattering (SAXS). Methods: Samples for cryo-EM were plunge frozen in liquid ethane with Vitrobot Mark IV and studied with Titan Krios (ThermoFisher Scientific, US) cryo-EM, equipped with Falcon 2 direct electron detector, Image corrector (CEOS, Germany), and Volta phase plate. Single Particle Analysis (SPA) and cryo-Electron Tomography (cryo-ET) studies were conducted with 300 kV accelerating voltage in low dose mode using EPU and Tomography software (ThermoFisher Scientific, US). Cryo-EM data processing was conducted using Warp, CryoSPARC, IMOD, EMAN, and Relion software packages. SAXS measurements were performed at the EMBL on the P12 BioSAXS beam line at the PETRAIII storage ring (DESY, Hamburg). Results: In this work, Dps-DNA complex formation is thoroughly studied using complementary cryo-EM (including SPA, cryo-ET, and subtomogram averaging) and SAXS methods. The formation of individual complexes of Dps with small linear DNA fragments and the Dps-Dps interaction was visualized using cryo-EM. It was found that Dps-DNA complex remains stable under various conditions and while the addition of different ions leads to the disruption of co-crystals, the process is completely or partially reversible. Conclusion: Recent studies conducted by our group showed that Dps-DNA co-crystals adopt triclinic or cubic crystal lattice (FEBS Lett., 2019; Biomolecules, 2020). Here we present the results on the studies of Dps interaction with small linear DNA fragments, demonstrate the effects of MgCl2, FeSO4, and EDTA on the Dps-DNA complex and individual Dps protein structure, discuss the influence of the temperature and time on the co-crystals

Review of laser scanning methods for microelectronic semiconductor structures investigation

The development and widespread of high-tech microelectronic products impose increased requirements on the quality and reliability of microcircuits. The most effective methods for reliability improvement of electronic systems include diagnostic non-destructive testing (NDT) methods and selective destructive testing in special cases. Studies using visual inspection and electrical testing, consisting of functional and parametric testing, do not provide enough information to detect latent defects (for example, macro-defects in SiO 2 layers in CMOS chips) and to detect fakes and counterfeits. A fake integrated circuit (IC) may contain an undeclared malicious modification of the circuit, called hardware bugs. The common ICs studying tools are systems based on microfocus X-ray sources, scanning acoustic microscopes, optical and scanning electron microscopes, and X-ray fluorescence spectroscopes. Products destruction avoidance is a fundamental point, for example, for the technological process control in crystal manufacturing. Investigation of ICs using a light microscope is one of the most accessible and widespread method of microchip NDT. Semiconductor ICs structure scanning from the side of the device layer is limited by the shielding effect of metallization, since the metal is opaque for light. This limitation can be overcome by an alternative approach to microchip scanning based on irradiating the IC from the side of the substrate with laser sources in the near-IR range. This paper provides a brief overview of the major methods used in laser scanning microscopy to analyze the structures, responses, and features of the operating modes of semiconductor circuits. The main advantages and limitations in the use of optical methods are described, as well as what information about the product can be obtained as a result of laser scanning

Application of machine vision technology for focused laser effect accuracy improvement in microelectronic structures research and semiconductor microprocessing

Machine vision is a field of artificial intelligence that deals with processing images and videos using special algorithms. This allows devices to analyze visual information. Machine vision helps with tasks such as pattern recognition, image segmentation, object detection, and tracking. In microscopy, machine vision plays an important role, particularly in laser scanning microscopy (LSM). Laser scanning microscopy, laser scribing, and laser correction of the topology of semiconductor crystals are important technological processes in the production, control and adjustment of semiconductor crystals both on debug samples and as part of a test batch on a wafer. Laser exposure allows not only mechanically separate crystals, but also carry out more delicate and minimally invasive actions, in particular, adjustments to the values of thin-film resistors or burning of bridges necessary to adjust the circuit and disable unused blocks of the crystal. The paper lists the main parameters of the positioning system as part of the laser scanning setup, their impact on the quality of scanning and exposure to focused radiation at control points. The principles of machine vision algorithms when working with the image of the scanned object and the results of testing in the task of automated laser burning of bridges on a semiconductor wafer are described. Since the number of bridges can reach tens of thousands, and positioning systems have significant errors, machine vision allows you to correct the area and accuracy of laser exposure at any stage of scanning, which significantly improves the quality and efficiency of the process

Structural Insights into Iron Ions Accumulation in Dps Nanocage

Dps (DNA-binding protein from starved cells) is well known for the structural protection of bacterial DNA by the formation of highly ordered intracellular assemblies under stress conditions. Moreover, this ferritin-like protein can perform fast oxidation of ferrous ions and subsequently accumulate clusters of ferric ions in its nanocages, thus providing the bacterium with physical and chemical protection. Here, cryo-electron microscopy was used to study the accumulation of iron ions in the nanocage of a Dps protein from Escherichia coli. We demonstrate that Fe2+ concentration in the solution and incubation time have an insignificant effect on the volume and the morphology of iron minerals formed in Dps nanocages. However, an increase in the Fe2+ level leads to an increase in the proportion of larger clusters and the clusters themselves are composed of discrete ~1–1.5 nm subunits

Hydroprocessing catalysts based on transition metal sulfides prepared from Anderson and dimeric Co2Mo10-heteropolyanions. A review

International audienceHydroprocessing catalysts based on transition metal sulfides have been extensively used worldwide in refineries for upgrading heavy fractions to better quality fuels. The present work reviews the studies dealing with Anderson heteropolyanions (HPAs) and the derived dimeric structure for synthesizing hydrotreating catalysts. The development of new preparation methods based on HPA catalysts led to efficient catalytic systems due to better sulfidation allowed by a better dispersion of the oxidic precursor even at high metallic loadings. The increase of the Co/Mo ratio in the heteropolycompounds up to 0.5 was possible due to the formation of dimer cobalt salt. The association of Co and Mo at the molecular level in the same heteropolycompound preserved after the drying step during the catalyst preparation ensured the efficiency of the promoting effect with a higher quantity of the CoMoS active phase. This HPA-based system was further improved by the simultaneous use of HPAs and chelating agents

Trimetallic Hydrotreating Catalysts CoMoW/Al2O3 and NiMoW/Al2O3 Prepared on the Basis of Mixed Mo-W Heteropolyacid: Difference in Synergistic Effects

International audienceTrimetallic CoMo3W9/Al2O3 catalyst is prepared using the Keggin structure mixed heteropolyacid H4SiMo3W9O40 and cobalt citrate. CoMo12/Al2O3 and CoW12/Al2O3 catalysts based on H4SiMo12O40 and H4SiW12O40, respectively, are synthesized as reference samples. Sulfided catalysts are analyzed by high-resolution transmission electron microscopy and X-ray photoelectron spectroscopy. Catalytic properties are investigated in the co-hydrotreatment of dibenzothiophene (DBT) and naphthalene in a flow unit. It is shown that the catalytic activity in both DBT hydrodesulfurization and naphthalene hydrogenation (HYD) decreases in the following sequence: CoMo12/Al2O3 > CoMo3W9/Al2O3 > CoW12/Al2O3, and it correlates with the degree of promotion of active-phase particles by cobalt atoms. A comparison with the published data available for Ni-promoted catalysts makes it possible to reveal the general regularity for bi- and trimetallic Со(Ni)-Mo(W)S catalysts: the use of mixed Mo-W H4SiMo3W9O40 heteropolyacid instead of monometallic H4SiW12O40 causes an increase in the degree of promotion of MoWS2 crystallite edges for the series of catalysts promoted by both cobalt and nickel. The use of nickel as a promoter leads to a higher degree of promotion of edges of active-phase particles in comparison with cobalt; as a result, the NiMo3W9/Al2O3 catalyst is much more active than the CoMo3W9/Al2O3 counterpart. Possible reasons behind the found features are discussed

Abstract OR-2: The Formation of Dps-DNA Complexes under Different Conditions According to Cryo-EM and SAXS

Background: The effect of Dps-DNA co-crystals formation, which occurs in stressed Escherichia coli cells exposed to extreme conditions, is well described in the literature. However, the exact mechanisms of co-crystals formation are yet to be postulated remaining largely unknown. Here we summarize the results obtained by our group over the last few years using cryo-Electron Microscopy (cryo-EM) and Small Angle X-ray Scattering (SAXS). Methods: Samples for cryo-EM were plunge frozen in liquid ethane with Vitrobot Mark IV and studied with Titan Krios (ThermoFisher Scientific, US) cryo-EM, equipped with Falcon 2 direct electron detector, Image corrector (CEOS, Germany), and Volta phase plate. Single Particle Analysis (SPA) and cryo-Electron Tomography (cryo-ET) studies were conducted with 300 kV accelerating voltage in low dose mode using EPU and Tomography software (ThermoFisher Scientific, US). Cryo-EM data processing was conducted using Warp, CryoSPARC, IMOD, EMAN, and Relion software packages..

New MoWS2/SBA-15 and MoWS2/COK-12 hydrotreating catalysts prepared by using SiMonW12-n heteropolyacids

International audienc