Stress‐response balance drives the evolution of a network module and its host genome

Stress response genes and their regulators form networks that underlie drug resistance. These networks often have an inherent tradeoff: their expression is costly in the absence of stress, but beneficial in stress. They can quickly emerge in the genomes of infectious microbes and cancer cells, protecting them from treatment. Yet, the evolution of stress resistance networks is not well understood. Here, we use a two‐component synthetic gene circuit integrated into the budding yeast genome to model experimentally the adaptation of a stress response module and its host genome in three different scenarios. In agreement with computational predictions, we find that: (i) intra‐module mutations target and eliminate the module if it confers only cost without any benefit to the cell; (ii) intra‐ and extra‐module mutations jointly activate the module if it is potentially beneficial and confers no cost; and (iii) a few specific mutations repeatedly fine‐tune the module's noisy response if it has excessive costs and/or insufficient benefits. Overall, these findings reveal how the timing and mechanisms of stress response network evolution depend on the environment

IR spectra of hydrated CaSO4 in the mid-infrared range

Background and Objectives: This work is devoted to the study of the influence of moisture of alabaster (building plaster) samples on the profiles of their IR spectra in the wave number range of 500–4000 cm−1. Materials and Methods: IR spectra of distilled water and alabaster samples with the moisture of 0, 26, 106, 132, 159, 185 and 212% at 23°C were investigated by experimental methods of disturbed total internal reflection. Wave numbers and intensities of components of IR spectra of CaSO4(H2O)n clusters for 0<n<16 were calculated by the methods based on density functional theory with exchange-correlation potential XLYP. Using Gaussian curves with the widths estimated from experiment, the profiles of water valence oscillation bands were determined. When calculating the structure of CaSO4(H2O)n, the positions of atoms in various structural modifications of clusters were optimized. The minimum total energy served as a criterion for choosing the optimal cluster structure, and for the clusters with a large number of atoms, this criterion was applied to an initially selected isomer. Conclusion: On the basis of the calculation results the transformations of the measured spectra (changes of wave numbers and intensities) with changes in the moisture content of the samples have been explained. Comparison of experimental and theoretical spectra in the 3500–3900 cm−1 range allowed to attribute the investigated alabaster powder to a combination of clusters of different sizes:2(CaSO4(H2O)0.5), 2(CaSO4(H2O)0.5 + 0.5H), 4(CaSO4(H2O)0.5), including a cluster of crystalline gypsum: 2(CaSO4(H2O)2). The achieved agreement in the the positions and profiles of the experimental and theoretical water bands in the spectra of samples of different moisture justifies the adequacy of the theoretical description of hydration of CaSO4. &nbsp

New palynological data for Toarcian (Lower Jurassic) deep-marine sandstones of the Western Caucasus, southwestern Russia

Information on Jurassic palynomorphs from the Greater Caucasus is potentially of great importance, but its availability to the international research community is severely limited. New palynological data for Toarcian deposits of the Western Caucasus are recorded in the present paper. Particularly, dinoflagellate cysts are described for the first time from the Bagovskaja Formation; palynomorphs are found in sandstone levels within this unit. The most representative assemblage includes pollen (with predominant bisaccate pollen), spores (Cyathidites being commonest), and dinoflagellate cysts amongst which the predominant taxon is Nannoceratopsis spiculata. The dinocyst assemblage implies a late Toarcian age for the upper part of the Bagovskaja Formation. On the basis of these new palynostratigraphical results, the range of the formation is extended; previously, only the lower part had been dated on ammonite evidence

Mechanism of Transcription Anti-termination in Human Mitochondria.

In human mitochondria, transcription termination events at a G-quadruplex region near the replication origin are thought to drive replication of mtDNA by generation of an RNA primer. This process is suppressed by a key regulator of mtDNA-the transcription factor TEFM. We determined the structure of an anti-termination complex in which TEFM is bound to transcribing mtRNAP. The structure reveals interactions of the dimeric pseudonuclease core of TEFM with mobile structural elements in mtRNAP and the nucleic acid components of the elongation complex (EC). Binding of TEFM to the DNA forms a downstream sliding clamp, providing high processivity to the EC. TEFM also binds near the RNA exit channel to prevent formation of the RNA G-quadruplex structure required for termination and thus synthesis of the replication primer. Our data provide insights into target specificity of TEFM and mechanisms by which it regulates the switch between transcription and replication of mtDNA

The luminescence of NaxEu3+(2−x)/3MoO4 scheelites depends on the number of Eu-clusters occurring in their incommensurately modulated structure

Scheelite related compounds with general formula Mn(XO4)m are of interest owing to their optical properties, stability and relatively simple preparation. Eu3+-containing scheelites are considered as red emitting phosphors and the main factors affecting their luminescence are thought to be chemical composition and particle size while the influence of their structure is generally ignored. Here we report eight compounds from the NaxEu(2_x)/3MoO4 series prepared by conventional solid-state reaction and present a detailed analysis of their crystal structures. Six of them have modulated structures, a common feature of SRCs, in which dopant Eu3+ ions are orderly distributed. Moreover, different amounts of Eu3+ dimers are detected in the modulated structures, characterized by weak satellite reflections appearing in the lower angle part of the XRD patterns. These reflections are indexed and incorporated into Rietveld’s refinement using superspace (3 + 1)-dimension symmetry. The remarkable feature of the compounds is that the characteristic luminescence parameters, overall and intrinsic quantum yields, Eu lifetimes, and sensitization efficiencies, correlate with the number of Eu3+ aggregates, but not directly with the composition x of the materials. This provides an efficient tool for understanding and controlling the luminescence properties of scheelite related compounds

Structure- and interaction-based design of anti-SARS-CoV-2 aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptorbinding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variant