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At least 1,297 records · Page 72

Plasmidic Expression of nemA and yafC * Increased Resistance of Ethanologenic Escherichia coli LY180 to Nonvolatile Side Products from Dilute Acid Treatment of Sugarcane Bagasse and Artificial Hydrolysate

Hydrolysate-resistant Escherichia coli SL100 was previously isolated from ethanologenic LY180 after sequential transfers in AM1 medium containing a dilute acid hydrolysate of sugarcane bagasse and was used as a source of resistance genes. Many genes that affect tolerance to furfural, the most abundant inhibitor, have been described previously. To identify genes associated with inhibitors other than furfural, plasmid clones were selected in an artificial hydrolysate that had been treated with a vacuum to remove furfural. Two new resistance genes were discovered from Sau3A1 libraries of SL100 genomic DNA: nemA (N-ethylmaleimide reductase) and a putative regulatory gene containing a mutation in the coding region, yafC *. The presence of these mutations in SL100 was confirmed by sequencing. A single mutation was found in the upstream regulatory region of nemR ( nemRA operon) in SL100. This mutation increased nemA activity 20-fold over that of the parent organism (LY180) in AM1 medium without hydrolysate and increased nemA mRNA levels >200-fold. Addition of hydrolysates induced nemA expression (mRNA and activity), in agreement with transcriptional control. NemA activity was stable in cell extracts (9 h, 37°C), eliminating a role for proteinase in regulation. LY180 with a plasmid expressing nemA or yafC * was more resistant to a vacuum-treated sugarcane bagasse hydrolysate and to a vacuum-treated artificial hydrolysate than LY180 with an empty-vector control. Neither gene affected furfural tolerance. The vacuum-treated hydrolysates inhibited the reduction of N -ethylmaleimide by NemA while also serving as substrates. In conclusion, expression of the nemA or yafC * plasmid in LY180 doubled the rate of ethanol production from the vacuum-treated sugarcane bagasse hydrolysate.

59 BASIC BIOLOGICAL SCIENCES↗

Refactoring the Genetic Code for Increased Evolvability

ABSTRACT The standard genetic code is robust to mutations during transcription and translation. Point mutations are likely to be synonymous or to preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best-performing mutant requires replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter a single nucleotide per mutation event, due to the extreme rarity of adjacent mutations. In this theoretical study, we suggest a radical reordering of the genetic code that maximizes the mutagenic potential of single nucleotide replacements. We explore several possible genetic codes that allow a greater degree of accessibility to the mutational landscape and may result in a hyperevolvable organism that could serve as an ideal platform for directed evolution experiments. We then conclude by evaluating the challenges of constructing such recoded organisms and their potential applications within the field of synthetic biology. IMPORTANCE The conservative nature of the genetic code prevents bioengineers from efficiently accessing the full mutational landscape of a gene via common error-prone methods. Here, we present two computational approaches to generate alternative genetic codes with increased accessibility. These new codes allow mutational transitions to a larger pool of amino acids and with a greater extent of chemical differences, based on a single nucleotide replacement within the codon, thus increasing evolvability both at the single-gene and at the genome levels. Given the widespread use of these techniques for strain and protein improvement, along with more fundamental evolutionary biology questions, the use of recoded organisms that maximize evolvability should significantly improve the efficiency of directed evolution, library generation, and fitness maximization.

59 BASIC BIOLOGICAL SCIENCES↗

Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance in Zymomonas mobilis

Genetically engineered microbes have the potential to increase efficiency in the bioeconomy by overcoming growth-limiting production stress. Screens of gene perturbation libraries against production stressors can identify high-value engineering targets, but follow-up experiments needed to guard against false positives are slow and resource-intensive. In principle, the use of orthogonal gene perturbation approaches could increase recovery of true positives over false positives because the strengths of one technique compensate for the weaknesses of the other, but, in practice, two parallel screens are rarely performed at the genome scale. Here, we screen genome-scale CRISPRi (CRISPR interference) knockdown and transposon insertion libraries of the bioenergy-relevant Alphaproteobacterium, Zymomonas mobilis, against growth inhibitors commonly found in deconstructed plant material. Integrating data from the two gene perturbation techniques, we established an approach for defining engineering targets with high specificity. This allowed us to identify all known genes in the cytochrome bc1 and cytochrome c synthesis pathway as potential targets for engineering resistance to phenolic acids under anaerobic conditions, a subset of which we validated using precise gene deletions. Strikingly, this finding is specific to the cytochrome bc1 and cytochrome c pathway and does not extend to other branches of the electron transport chain. We further show that exposure of Z. mobilis to ferulic acid causes substantial remodeling of the cell envelope proteome, as well as the downregulation of TonB-dependent transporters. Our work provides a generalizable strategy for identifying high-value engineering targets from gene perturbation screens that is broadly applicable.

CRISPRi↗

Increase in the Fluorine-Ion Conductivity of Single Crystals of Tysonite-type CeF{sub 3} Superionic Conductor by Substituting Polarized Cd{sup 2+} Ions for Ce{sup 3+} Ions

The fluorine-ion conductivity of single crystals with a tysonite (LaF{sub 3}) structure with heterovalent isomorphic substitutions of highly polarizable Cd{sup 2+} cations with a 18-electron shell for rare earth ions Ce{sup 3+} have been studied for the first time. Ce{sub 0.995}Cd{sub 0.005}F{sub 2.995} single crystals have been grown from melt by the Bridgman technique in a fluorinating atmosphere. The fluorine-ion conductivity of single crystal is measured by impedance spectroscopy in the temperature range from 153 to 1073 K, where it increases by a factor of 10{sup 9}, approaching the value σ{sub dc} = 5 × 10{sup –2} S/cm at 1073 K. At T{sub 0} = 450 ± 20 K, the dependence σ{sub dc}(T) is split into two portions with the ion-transport activation enthalpy ΔH{sub σ} = 0.39 ± 0.01 eV (T < T{sub 0}) and ΔH{sub σ} = 0.23 ± 0.02 eV (T > T0). It is found that at T = 293 K the conductivity σ{sub dc} = 3 × 10{sup –5} S/cm of Ce{sub 0.995}Cd{sub 0.005}F{sub 2.995} crystal is higher by a factor of 10 than the conductivity of the tysonite matrix CeF{sub 3} and close to the σ{sub dc} value for Ce{sub 0.995}Sr{sub 0.005}F{sub 2.995} crystal. This finding indicates a significant effect of the substitutions of Cd{sup 2+} ions for Ce{sup 3+} on the σdc value and the advantage of Cd{sup 2+} ions over Ca{sup 2+} and Ba{sup 2+} from the viewpoint of increasing σ{sub dc}.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Cathodo- and photoluminescence increase in amorphous hafnium oxide under annealing in oxygen

Cathodo- and photoluminescence of amorphous nonstoichiometric films of hafnium oxide are studied with the aim to verify the hypothesis that oxygen vacancies are responsible for the luminescence. To produce oxygen vacancies, hafnium oxide was enriched in surplus metal during synthesis. To reduce the oxygen concentration, the film was annealed in oxygen. A qualitative control of the oxygen concentration was carried out by the refractive index. In the initial, almost stoichiometric films we observed a 2.7-eV band in cathodoluminescence. Annealing in oxygen results in a considerable increase in its intensity, as well as in the appearance of new bands at 1.87, 2.14, 3.40, and 3.6 eV. The observed emission bands are supposed to be due to single oxygen vacancies and polyvacancies in hafnium oxide. The luminescence increase under annealing in an oxygen atmosphere may be a result of the emission quenching effect.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Exponential Increase in the Resistivity upon Cooling and Superconductivity in Indium-Doped Pb{sub 0.45}Sn{sub 0.55}Te

We have analyzed the temperature and magnetic-field dependences of resistivity ρ(T, H) of semiconducting compound Pb{sub 0.45}Sn{sub 0.55}Te doped with 5 at % In under a hydrostatic compression at P < 12 kbar. It is found that the temperature dependence ρ(T) at all pressures at T < 100 K is exponential with the activation energy decreasing upon an increase in pressure; this is accompanied with a superconducting transition on the ρ(T) and ρ(H) dependences at P > 4.8 kbar at T > 1 K (T{sub c} = 1.72 K at a level of 0.5ρ{sub N} at P = 6.8 kbar). We consider the model describing the low-temperature “dielectrization” of the semiconducting solid solution and the formation of the superconducting state upon an increase in the hydrostatic compression P > 4 kbar.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The concept of the use of recycled uranium for increasing the degree of security of export deliveries of fuel for light-water reactors

The present paper deals with investigation of the possibilities for reducing the risk of proliferation of fissionable materials by means of increasing the degree of protection of fresh fuel intended for light-water reactors against unsanctioned use in the case of withdrawal of a recipient country of deliveries from IAEA safeguards. It is shown that the use of recycled uranium for manufacturing export nuclear fuel makes transfer of nuclear material removed from the fuel assemblies for weapons purposes difficult because of the presence of isotope {sup 232}U, whose content increases when one attempts to enrich uranium extracted from fresh fuel. In combination with restricted access to technologies for isotope separation by means of establishing international centers for uranium enrichment, this technical measure can significantly reduce the risk of proliferation associated with export deliveries of fuel made of low-enriched uranium. The assessment of a maximum level of contamination of nuclear material being transferred by isotope {sup 232}U for the given isotope composition of the initial fuel is obtained. The concept of further investigations of the degree of security of export deliveries of fuel assemblies with recycled uranium intended for light-water reactors is suggested.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

How to increase the efficiency of the electrical discharge method for destruction of nonconductive solid materials

The paper deals with the relevance of using electrical discharge technology for construction works in the city. The technical capabilities of the installation for the multi-borehole electro-discharge splitting off and destruction of rocks and concrete are described. The ways to increase the efficiency of the electrical discharge method for the destruction of solids are proposed. In order to augment the discharge circuit energy, the energy storage is separated into two individual capacitor batteries. The throttle with the inductance of 28.6 μH is installed in one of the batteries, which increases the duration of the channel energy release to 400 μs and the efficiency of electrical discharge splitting off of concrete.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

On the feasibility of increasing the energy of laser-accelerated protons by using low-density targets

Optimal regimes of proton acceleration in the interaction of short high-power laser pulses with thin foils and low-density targets are determined by means of 3D numerical simulation. It is demonstrated that the maximum proton energy can be increased by using low-density targets in which ions from the front surface of the target are accelerated most efficiently. It is shown using a particular example that, for the same laser pulse, the energy of protons accelerated from a low-density target can be increased by one-third as compared to a solid-state target.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Increase of the electron mobility in HEMT heterostructures with composite spacers containing AlAs nanolayers

The effect of the hybridization of quantum states on electron transport in a two-barrier quantum well δ-doped through a spacer layer at the limit of heavy doping is shown theoretically and experimentally. A method for increasing the electron mobility in the quantum well by suppressing the tunnel coupling with the donor region through the introduction of an AlAs nanobarrier into the spacer layer is proposed. It is experimentally shown that, in the samples with a shallow quantum well, the AlAs nanobarrier introduced into the spacer layer provides a larger than threefold increase in the electron mobility at low temperatures.

36 MATERIALS SCIENCE↗

Increase in the Shockley–Read–Hall recombination rate in InGaN/GaN QWs as the main mechanism of the efficiency droop in LEDs at high injection levels

It is shown that the efficiency droop observed as the current through a GaN-based light-emitting diode increases is due to a decrease in the Shockley–Read–Hall nonradiative lifetime. The lifetime decreases with increasing current because a steadily growing number of traps in the density-of-states tails of InGaN/GaN quantum wells become nonradiative recombination centers upon the approach of quasi-Fermi levels to the band edges. This follows from the correlation between the efficiency droop and the appearance of negative differential capacitance, observed in the study. The correlation appears due to slow trap recharging via the trap-assisted tunneling of electrons through the n-type barrier of the quantum well and to the inductive nature of the diode-current variation with forward bias.

36 MATERIALS SCIENCE↗

Effect of an increase in the density of collision cascades on the efficiency of the generation of primary displacements during the ion bombardment of Si

The depth distributions of structural damage induced in Si at room temperature by the implantation of P and PF{sub 4} with energies from 0.6 to 3.2 keV/amu are experimentally studied in a wide range of doses. It is found that, in all cases, the implantation of molecular PF{sub 4} ions forms practically single-mode defect distributions, with maximum at the target surface. This effect is caused by an increase in the generation of primary defects at the surface of the target. Individual cascades formed by atoms comprising molecule effectively overlap in the surface vicinity; this overlap gives rise to nonlinear processes in combined cascades due to a high density of displacements in such cascades. Quantitative estimation of increase of effectiveness of point defect generation by PF{sub 4} ions in respect to P ions is done on the base of experimental data.

36 MATERIALS SCIENCE↗

Increasing the Luminescence Yield of Zirconia

The effect of high-temperature treatment in vacuum in the presence of carbon as a reducing agent on the luminescent properties of zirconia is studied. It is shown that an increase in the intensity of pulsed cathodoluminescence at 480 nm and thermoluminescence in the dominant peak at 500 K is due to the thermochemical coloration of the initial samples with the formation of oxygen vacancies detected by electron paramagnetic resonance. The described procedure for increasing the luminescence yield of ZrO{sub 2} can be applied when it is used in optoelectronics, photonics, and radiation dosimetry.

36 MATERIALS SCIENCE↗

Nonmonotonic Change in the Tunnel Conductivity of an MIS Structure with a Two-Layer Insulator with an Increase in Its Thickness (by the Example of the Metal/SiO{sub 2}/CaF{sub 2}/Si System)

The effect of increasing the tunnel current in a metal–calcium fluoride–silicon structure with addition of a silicon dioxide layer between fluoride and metal (which seems paradoxical at first glance) has been considered. This effect of nonmonotonic change in the tunnel conductivity with an increase in the insulator thickness may occur at a relatively high bias at the structure and is related to the tunnel-barrier deformation, at which electrons are tunneling through its part formed by the oxide. At low biases, the occurrence/ thickening of an additional layer leads to a natural decrease in the current. Similar behavior is possible in principle for some other combinations of materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Localization of Upper-Valley Electrons in a Narrow-Bandgap Channel: a Possible Additional Mechanism of Current Increase in DA–DpHEMT

The influence of the localization of upper-valley electrons in a narrow-bandgap channel on the drift velocity burst in Al{sub x}Ga{sub 1 –x}As–GaAs transistor heterostructures with double-sided doping has been theoretically estimated. It is established that the fraction of electrons passing in this case from the narrow-bandgap channel to wide-bandgap material is smaller than in the usual structures, which can lead in some cases to an increase in the electron drift velocity by up to 15%. This phenomenon can provide an additional mechanism of current increase in transistors based on heterostructures with donor–acceptor doping.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Identification of stress biomarkers for drought and increased soil temperature in seedlings of European beech ( Fagus sylvatica )

Drought is an environmental stress that impacts plant productivity. Projections show both an increase in intense rain events and a reduction in the number of rain days, conditions that leads to increased risk of drought. Consequently, the identification of molecular biomarkers suitable for evaluating the impact of water deprivation conditions on forest plant seedlings is of significant value for monitoring purposes and forest management. In this study, we evaluated a biochemical methodology for the assessment of drought stress coupled with variable soil temperature in European beech (Fagus sylvatica L.) seedlings by analyzing a set of metabolites and enzymes involved in free radical scavenging and cell wall synthesis. The results indicate that the specific activities and isoform profile of superoxide dismutases and glutathione peroxidases together with the variation of phenolic compounds enable discrimination between seedlings with different degrees of photosynthetic activity. This approach represents a promising platform for the assessment of drought stress in forest trees and could serve for enhancing selection and breeding practices, allowing for plants that are more tolerant of abiotic stress.

beach↗

Increasing the Measured Effective Quantum Volume with Zero Noise Extrapolation

Quantum volume is a full-stack benchmark for near-term quantum computers. It quantifies the largest size of a square circuit which can be executed on the target device with reasonable fidelity. Error mitigation is a set of techniques intended to remove the effects of noise present in the computation of noisy quantum computers when computing an expectation value of interest. Effective quantum volume is a proposed metric that applies error mitigation to the quantum volume protocol to evaluate the effectiveness not only of the target device but also of the error mitigation algorithm. Digital zero-noise extrapolation is an error mitigation technique that estimates the noiseless expectation value using circuit folding to amplify errors by known scale factors and then extrapolating computed expectation values to the zero-noise limit. Here we demonstrate that zero-noise extrapolation, with global and local unitary folding with fractional scale factors, in conjunction with dynamical decoupling, can increase the effective quantum volume over the vendor-measured quantum volume. Specifically, we measure the effective quantum volume of four IBM Quantum superconducting processor units, obtaining values that are larger than the vendor-measured quantum volume on each device. This is the first such increase reported.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Apparent Increasing Lithium Diffusion Coefficient with Applied Current in Graphite

In this study, we assert that the apparent lithium diffusion coefficient in graphite active particles in the negative electrodes of lithium-ion cells increases appreciably with the intercalation rate. This assertion is based on an electrochemical model analysis of a wide range of electrochemical micro-reference electrode full cell studies on a coated natural graphite and other literature results. Although the mechanism for this increase is a subject of further investigation, the results of our study suggest that the lithium transport in the graphite does not limit the maximum attainable charging rate in typical lithium-ion cells for electric vehicles.

25 ENERGY STORAGE↗