Hengzongshu/ArticleAgent huggingface dataset:
In contrast to proteins recognizing small-molecule ligands, DNA-dependent enzymes cannot rely solely on interactions in the substrate-binding centre to achieve their exquisite specificity. It is widely believed that substrate recognition by such enzymes involves a series of conformational changes in the enzyme–DNA complex with sequential gates favoring cognate DNA and rejecting nonsubstrates. However, direct evidence for such mechanism is limited to a few systems.

We report that discrimination between the oxidative DNA lesion, 8-oxoguanine (oxoG) and its normal counterpart, guanine, by the repair enzyme, formamidopyrimidine-DNA glycosylase (Fpg), likely involves multiple gates. Fpg uses an aromatic wedge to open the Watson–Crick base pair and everts the lesion into its active site. We used molecular dynamics simulations to explore the eversion free energy landscapes of oxoG and G by Fpg, focusing on structural and energetic details of oxoG recognition. The resulting energy profiles, supported by biochemical analysis of site-directed mutants disturbing the interactions along the proposed path, show that Fpg selectively facilitates eversion of oxoG by stabilizing several intermediate states, helping the rapidly sliding enzyme avoid full extrusion of every encountered base for interrogation.

Lesion recognition through multiple gating intermediates may be a common theme in DNA repair enzymes.
Horizontal transfer (HT) is a complex phenomenon usually used as an explanation of phylogenetic inconsistence, which cannot be interpreted in terms of vertical evolution. Most examples of HT of eukaryotic genes involve transposable elements. An intriguing feature of HT is that its frequency differs among transposable elements classes. Although HT is well known for DNA transposons and long terminal repeat (LTR) retrotransposons, non-LTR retrotransposons rarely undergo HT, and their phylogenies are largely congruent to those of their hosts. Previously, we described HT of CR1-like non-LTR retrotransposons between butterflies (Maculinea) and moths (Bombyx), which occurred less than 5 million years ago (Novikova O, Sliwinska E, Fet V, Settele J, Blinov A, Woyciechowski M. 2007. CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission. BMC Evol Biol. 7:93). In this study, we continued to explore the diversity of CR1 non-LTR retrotransposons among lepidopterans providing additional evidences to support HT hypothesis. We also hypothesized that DNA transposons could be involved in HT of non-LTR retrotransposons. Thus, we performed analysis of one of the groups of DNA transposons, mariner-like DNA elements, as potential vectors for HT of non-LTR retrotransposons. Our results demonstrate multiple HTs between Maculinea and Bombyx genera. Although we did not find strong evidence for our hypothesis of the involvement of DNA transposons in HT of non-LTR retrotransposons, we demonstrated that recurrent and/or simultaneous flow of TEs took place between distantly related moths and butterflies.
A numerical and experimental study of the spectral distribution of disturbances hotshot wind tunnel was performed. It was found that disturbances are the superposition of fast acoustic waves propagating along axial direction and oblique slow acoustic waves which have less amplitude. Numerical simulation of disturbances evolution in the nozzle of the wind tunnel was carried out by solving 2D Navier-Stokes equations using the ANSYS Fluent program package. Experiments were carried out in the IT-302M high-enthalpy hotshot wind tunnel ITAM SB RAS.
Recently, much attention has been paid to reducing environmental damage to the environment throughout the country. Over the past twenty years, Public Joint-Stock Company "Gazprom" has been working on the implementation of environmental projects for the transfer of motor vehicles to alternative motor fuels. The report suggests a toolkit for assessing the impact of energy saving projects on the environment, based on the adaptation of the input-output model for the fuel and energy complex. The model is based on the assumption that the main amount of greenhouse gas emissions is produced by burning fossil fuels. As an indicator for estimation of environmental efficiency of the projects has proposed the coefficient of carbon intensity - the amount of carbon dioxide released per unit of the final product of the industry. This ratio reflects the impact of industries on the environment. The advantage of the input-output model is the opportunity to conduct a comparative analysis of the environmental load of industries on the environment and to determine the multiplicative effect of implementing energy-saving projects.
Background.The end-use of the bread wheat grain depends on the endosperm properties determined by the alleles of the Pinaand Pinbgenes at the Halocus on chromosome 5D. The mealy (soft) endosperm is generated by the biosynthesis of puroindolines – complete proteins encoded by these genes. When milled, such grain breaks down into small starch granules covered with proteins. Mutations that disrupt the synthesis or structure of puroindolines determine the hardness and vitreousness of the grain. Earlier, we discovered a new locus for grain softness, Ha-Sp, introgressed from the diploid species Aegilops speltoidesTausch, which also determines the formation of the soft endosperm structure. By combining two active loci in one genotype, we produced a supersoft grain line (SSL). The aim of the present work was to verify the interaction of the two loci Haand HaSpin other wheat genotypes and evaluate the technological properties of grain and flour in comparison with the existing SSL line. Materials and methods.The F3–F8 hybrids from crosses of the soft-grain spring cultivars ‘Golubka’ and ‘Lutescens 62’, carriers of the Halocus, with the introgressive line 84/98w, carrier of the Ha-Splocus, were used in the work. Grain from three field seasons was studied according to milling parameters and physical properties of flour and dough. Results.At the early stages of selection (F3:4), the families with milling parameters typical of bread wheat were identified, as well as supersoft-grain families with a small flour particle size (9–10 μm) and low endosperm vitreousness (29–49%). Targeted selection made it possible to obtain lines similar to the SSL line in terms of milling performance and flour strength. Conclusion.For the first time, a set of supersoft-grain lines with special properties of grain and flour was obtained on the genetic basis of three spring cultivars. They may be in demand for a wide range of end-uses, including both food and nonfood production purposes.
As plants are sessile organisms unable to escape from environmental hazards, they need to adapt for survival. The stem cell niche in the root apical meristem is particularly sensitive to DNA damage induced by environmental stresses such as chilling, flooding, wounding, UV, and irradiation. DNA damage has been proven to cause stem cell death, with stele stem cells being the most vulnerable.

Stress also induces the division of quiescent center cells. Both reactions disturb the structure and activity of the root stem cell niche temporarily; however, this preserves root meristem integrity and function in the long term.

Plants have evolved many mechanisms that ensure stem cell niche maintenance, recovery, and acclimation, allowing them to survive in a changing environment. Here, we provide an overview of the cellular and molecular aspects of stress responses in the root stem cell niche.
Objective: to study the association of the polymorphic genotypes of rs4680 in the catechol-O-methyl transferase (COMT) gene with vital exhaustion (VE) in a 45–64-year-old population.

Patients and methods. A representative sample of a 45–64-year-old population (781 men and 869 women) was surveyed within screening IV of the international Health, Alcohol and Psychological Factors in Eastern Europe (HAPIEE) program and the WHO MONICA-psychosocial program in 2003-2005. All the study participants filled out a VE scale of the WHO MONICA-psychosocial program. COMT Val158Met (rs4680) polymorphism was genotyped. Pearson' χ 2 test was used to test the statistical significance of differences between these groups. The statistical significance level was taken to be p≤0.05 in all types of analysis.

Results and discussion. Heterozygous G/A polymorphism in the COMT gene was most common in both the general population (48.6%) and men (44.4%) and women (51.5%). In the general population, the A/A genotype was more common in individuals with a high VE (HVE) level; in women and men, it was detected in 13.3 and 30.8% of cases, respectively. The G/G genotype prevailed in individuals with moderate VE in both the general population (31.1%) and women (29.7%) and men (33.3%). Conclusion. In the general population, the A/A genotype was found to be more common in individuals with HVE (18.6%), in women (13.3) and in men (30.8%).
In most phylogenetic lineages, the evolution of sex chromosomes is accompanied by their heteromorphization and degradation of one of them. The neo-sex chromosomes are useful model for studying early stages of these processes. Recently two lineages of the neo-sex chromosomes on different stages of heteromorphization was discovered in Pamphagidae family.

The neo-sex chromosome heteromorphization was analyzed by generation of DNA probes derived from the neo-Xs and neo-Ys followed with chromosome painting in nineteen species of Pamphagidae family. The homologous regions of the neo-sex chromosomes were determined in closely related species with the painting procedure and image analysis with application of the Visualization of the Specific Signal in Silico software package.

Results of these analyses and distribution of C-positive regions in the neo-sex chromosomes revealed details of the heteromorphization of the neo-sex chromosomes in species from both phylogenetic lineages of Pamphagidae grasshoppers. The hypothetical mechanism of the neo-Y degradation was suggested. It includes expansion of different repeats from the proximal neo-Y chromosome region by inversions, spreading them towards distal region. Amplification of these repeats leads to formation of C-positive regions and elimination of the C-negative regions located between them.
ABSTRACT Background Oxidative stress plays an important role in the development of neurodegenerative diseases: it either can be the initiator or part of a pathological cascade leading to the neuron’s death. Although a lot of methods are known for oxidative stress study, most of them operate on non-native cellular substrates or interfere with the cell functioning. Genetically encoded (GE) biosensors of oxidative stress demonstrated their general functionality and overall safety in various live systems. However, there is still insufficient data regarding their use for research of disease-related phenotypes in relevant model systems, such as human cells. Methods We applied CRISPR/Cas9 genome editing to introduce mutations (c.272A>C and c.382G>C) in the associated with amyotrophic lateral sclerosis SOD1 gene of induced pluripotent stem cells (iPSC) obtained from a healthy individual. Using CRISPR/Cas9, we modified these mutant iPSC lines, as well as the parental iPSC line, and a patient-specific SOD1 D91A/D91A iPSC line with ratiometric GE biosensors of cytoplasmic (Cyto-roGFP2-Orp1) and mitochondrial (Mito-roGFP2-Orp1) H 2 O 2 . The biosensors sequences along with a specific transactivator for doxycycline-controllable expression were inserted in the “safe harbor” AAVS1 (adeno-associated virus site 1) locus. We differentiated these transgenic iPSCs into motor neurons and investigated the functionality of the biosensors in such a system. We measured relative oxidation in the cultured motor neurons and its dependence on culture conditions, age, and genotype, as well as kinetics of H 2 O 2 elimination in real-time. Results We developed a cell-based platform consisting of isogenic iPSC lines with different genotypes associated with amyotrophic lateral sclerosis. The iPSC lines were modified with GE biosensors of cytoplasmic and mitochondrial H 2 O 2 . We provide proof-of-principle data showing that this approach may be suitable for monitoring oxidative stress in cell models of various neurodegenerative diseases as the biosensors reflect the redox state of neurons. Conclusion We found that the GE biosensors inserted in the AAVS1 locus remain functional in motor neurons and reflect pathological features of mutant motor neurons, although the readout largely depends on the severity of the mutation.
A graph is called Hamiltonian connected graph if for every pair of distinct vertices , ∈ () there exists a hamiltonian (, )-path in .

In this paper we prove Hamiltonian connectivity of the family of infinite two-dimensional diagonal grid induced subgraphs with added horizontal and vertical border edges.A generalization for multidimensional case is given.

These results are applied to prove the existence of discrete dynamic systems with arbitrary control functions with some given functioning properties.
Abnormalities in functioning of the central serotonergic system are believed to be involved in the pathogenesis of depressive illness and suicidal behaviour. Tryptophan hydroxylase (TPH) is a rate-limiting enzyme in the biosynthesis of serotonin, so the TPH gene (11p15.3-p14) is a good candidate for association studies with suicide. Several polymorphisms in the TPH gene have been studied for association with suicidal behaviour, but the results are inconclusive.

The aim of the present study is to determine whether the TPH gene is a susceptibility factor for suicidal behaviour in males and females, separately.
We present a search for seven lepton-flavor-violating neutral charm meson decays of the type D0→X0e±μ∓, where X0 represents a π0, K0S, ¯K*0, ρ0, ϕ, ω, or η meson. The analysis is based on 468 fb−1 of e+e− annihilation data collected at or close to the Υ(4S) resonance with the BABAR detector at the SLAC National Accelerator Laboratory. No significant signals are observed, and we establish 90% confidence level upper limits on the branching fractions in the range (5.0−22.5)×10−7. The limits are between 1 and 2 orders of magnitude more stringent than previous measurements.Received 21 April 2020Accepted 26 May 2020DOI:https://doi.org/10.1103/PhysRevD.101.112003Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI. Funded by SCOAP3.Published by the American Physical SocietyPhysics Subject Headings (PhySH)PropertiesSymmetriesParticles & Fields
Background Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology. Methods We characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore Beroe ovata using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species. Results The protist belongs to the genus Thraustochytrium based on the 18S rRNA sequence analysis. We designated the isolated protist as T. aureum ssp. strugatskii . The closest species with the genome assembly is Schizochytrium aggregatum . Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes. Conclusion Our findings suggest that the T. aureum ssp. strugatskii is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families.
A finite group G is called Schur, if every Schur ring over G is associated in a natural way with a regular subgroup of sym (G) that is isomorphic to G. We prove that any non-abelian Schur group G is metabelian and the number of distinct prime divisors of the order of G does not exceed 7.
The ability to solve problems of divergent type is one of the most intact functions in successful aging. However, neurophysiologic mechanisms that support the efficiency of creative thinking remain largely unknown.

This study was aimed to investigate age-related difference in localized induced electroencephalogram (EEG) changes during creative idea evaluation stage of divergent problem-solving (Alternate Uses Task), using standardized low-resolution brain electromagnetic tomography. Younger (45 women, 44 men, M age = 22.1 years, age range: 18–30 years) and older adults (46 women, 43 men, M age = 64.9 years, age range: 55–75 years) participated in the study. Higher synchronization in individually adjusted theta frequency band [from (individual alpha peak frequency −6 Hz) to (individual alpha peak frequency −4 Hz)] in anterior areas with the maximum values in anterior cingulate gyrus was revealed in older as compared with younger participants by group contrast. Higher desynchronization in wide beta range [from (individual alpha peak frequency +2 Hz) to 30 Hz] was localized in posterior brain regions with the highest values in posterior cingulate gyrus, precuneus, and parietal lobule in older adults.

Induced beta 2 synchronization was positively correlated with originality (as measured by the mean frequency of ideas) in younger and years of education in older subjects. Based on the data, it was supposed that controlling the decision-making processes is more important for older adults while maintenance of the internal image of elements’ recombination may play essential role for younger subjects.
One of the mechanisms of generation of powerful pressure pulsations in the circuit of the turbine is a precessing vortex core, formed behind the runner at the operation points with partial or forced loads, when the flow has significant residual swirl. To study periodic pressure pulsations behind the runner the authors of this paper use approaches of experimental modeling and methods of computational fluid dynamics. The influence of velocity distributions at the output of the hydro turbine runner on pressure pulsations was studied based on analysis of the existing and possible velocity distributions in hydraulic turbines and selection of the distribution in the extended range. Preliminary numerical calculations have showed that the velocity distribution can be modeled without reproduction of the entire geometry of the circuit, using a combination of two blade cascades of the rotor and stator. Experimental verification of numerical results was carried out in an air bench, using the method of 3D-printing for fabrication of the blade cascades and the geometry of the draft tube of hydraulic turbine. Measurements of the velocity field at the input to a draft tube cone and registration of pressure pulsations due to precessing vortex core have allowed building correlations between the velocity distribution character and the amplitude-frequency characteristics of the pulsations.
A molecular dynamics simulation approach was applied for the prediction of the thermal stability of oligonucleotide duplexes. It was shown that the enthalpy of the DNA/DNA complex formation could be calculated using this approach. We have studied the influence of various simulation parameters on the secondary structure and the hybridization enthalpy value of Dickerson–Drew dodecamer. The optimal simulation parameters for the most reliable prediction of the enthalpy values were determined.

The thermodynamic parameters (enthalpy and entropy changes) of a duplex formation were obtained experimentally for 305 oligonucleotides of various lengths and GC-content. The resulting database was studied with molecular dynamics (MD) simulation using the optimized simulation parameters. Gibbs free energy changes and the melting temperatures were evaluated using the experimental correlation between enthalpy and entropy changes of the duplex formation and the enthalpy values calculated by the MD simulation.

The average errors in the predictions of enthalpy, the Gibbs free energy change, and the melting temperature of oligonucleotide complexes were 11%, 10%, and 4.4 °C, respectively. We have shown that the molecular dynamics simulation gives a possibility to calculate the thermal stability of native DNA/DNA complexes a priori with an unexpectedly high accuracy.
A counter-intuitive disappearance of the giant terahertz photoconductance of a quantum point contact (QPC) under increase in the photon energy, which was discovered experimentally (Otteneder et al., Phys. Rev. Applied 10 (2018) 014015) and studied by the numerical calculations of the photon-stimulated transport (O.A. Tkachenko et al., JETP Lett. 108 (2018) 396), is explained here by using qualitative considerations about the momentum conservation upon absorption of terahertz photons. The spectra of photon-stimulated transmission through a smooth one-dimensional barrier are calculated on the basis of the perturbation theory. These calculations also predict the spectral maxima for optical transitions from the Fermi level to the top of the potential barrier. Within the proposed physical picture, the widths of the spectral maxima are estimated, and the evolution of the shape of the spectra with a change in the position of the Fermi level is qualitatively explained.
In order to clarify the origin of spring growth habit in modern domesticated wheat, allelic variability of the VRN-1 gene was investigated in a wide set of accessions of the wild tetraploid species Triticum dicoccoides (BBAA), together with diploid species T. monococcum, T. boeoticum and T. urartu, presumable donors of the A genome to polyploid wheats.

No significant variation was found at the VRN-B1 locus of T. dicoccoides, whereas at VRN-A1 a number of previously described alleles were found with small deletions in the promoter (VRN-A1b, VRN-A1d) or a large deletion in the first (1st) intron (VRN-A1L). The diploid A genome species were characterized by their own set of VRN-1 alleles including previously described VRN-A1f and VRN-A1h alleles with deletions in the promoter region and the VRN-A1ins allele containing a 0.5 kb insertion in the 1st intron. Based on the CAPS screening data, alleles VRN-A1f and VRN-A1ins were species-specific for T. monococcum, while allele VRN-A1h was specific for T. boeoticum. Different indels were revealed in both the promoter and 1(st) intron of the recessive VRN-A1u allele providing specific identification of T. urartu, the proposed donor of the A genome to modern wheat.

We found that alleles VRN-A1b and VRN-A1h, previously described as dominant, have either no or weak association with spring growth habit, while in some diploid accessions this habit was associated with the recessive VRN-A1 allele.Spring growth habit in diploid wheats was only partially associated with indels in regulatory regions of the VRN-1 gene. An exception is T. monococcum where dominant mutations in both the promoter region and, especially, the 1st intron were selected during domestication resulting in a greater variety of spring forms. The wild tetraploid T. dicoccoides had a distinct set of VRN-A1 alleles compared to the diploids in this study, indicating an independent origin of spring tetraploid forms that likely occurred after combining of diploid genomes. These alleles were subsequently inherited by cultivated polyploid (tetraploid and hexaploid) descendants.