Hengzongshu/ArticleAgent huggingface dataset:
Bacteriophages are known to be one of the driving forces of bacterial evolution. Besides promoting horizontal transfer of genes between cells, they may induce directional selection of cells (for instance, according to more or less resistance to phage infection). Switching between lysogenic and lytic pathways results in various types of (co)evolution in host-phage systems. Spatial (more generally, ecological) organization of the living environment is another factor affecting evolution. In this study, we have simulated and analyzed a series of computer models of microbial communities evolving in spatially distributed environments under the pressure of phage infection.We modeled evolving microbial communities living in spatially distributed flowing environments. Non-specific nutrient supplied in the only spatial direction, resulting in its non-uniform distribution in environment. We varied the time and the location of initial phage infestation of cells as well as switched chemotaxis on and off. Simulations were performed with the Haploid evolutionary constructor software ( http://evol-constructor.bionet.nsc.ru/ ).Simulations have shown that the spatial location of initial phage invasion may lead to different evolutionary scenarios. Phage infection decreases the speciation rate by more than one order as far as intensified selection blocks the origin of novel viable populations/species, which could carve out potential ecological niches. The dependence of speciation rate on the invasion node location varied on the time of invasion. Speciation rate was found to be lower when the phage invaded fully formed community of sedentary cells (at middle and late times) at the species-rich regions. This is especially noticeable in the case of late-time invasion. Our simulation study has shown that phage infection affects evolution of microbial community slowing down speciation and stabilizing the system as a whole. This influencing varied in its efficiency depending on spatially-ecological factors as well as community state at the moment of phage invasion.
Mongolian goats are of great interest for studying ancient migration routes and domestication, and also represent a good model of adaptability to harsh environments. Recent climatic disasters and uncontrolled massive breeding endangered the valuable genetic resources of Mongolian goats and raised the question of their conservation status. Meanwhile, Mongolian goats have never been studied on genomic scale. We used Illumina Goat SNP50 to estimate genetic risks in five Mongolian goat breeds (Buural, Ulgii Red, Gobi GS, Erchim, Dorgon) and explored phylogenic relationships among these populations and in the context of other breeds. Various clustering methods showed that Mongolian goats grouped with other Asian breeds and were especially close to some neighboring Russian and Chinese breeds. The Buural breed showed the lowest estimates of inbreeding and exhibited the shortest genetic distances within the other Mongolian breeds, especially, to Ulgii Red and Gobi GS. These three breeds formed a single core group, being weakly differentiated from each other. Among them, Gobi GS displayed obvious signs of inbreeding probably resulted from artificial selection pressure. Dorgon and especially Erchim goats stand apart from the other Mongolian breeds according to various types of analyses, and bear unique features pointing to different breeding histories or distinct origins of these breeds. All populations showed strong decline in effective population size. However, none of them met formal criteria to be considered as endangered breeds. The SNP data obtained in this study improved the knowledge of Mongolian goat breeds and could be used in future management decisions in order to preserve their genetic diversity.
Double‐walled carbon nanotubes (DWCNTs) have been fluorinated by pure molecular fluorine (F 2 ) at room temperature or 200 °C and a mixture of F 2 with hydrogen fluoride (HF) at 200 °C that resulted in products with compositions of CF 0.12 , CF 0.39 , and CF 0.53 as determined by X‐ray photoelectron spectroscopy. The differences in the structures of three kinds of fluorinated DWCNTs were revealed using transmission electron microscopy, Raman scattering, and near‐edge X‐ray absorption fine structure (NEXAFS) spectroscopy. Quantum‐chemical modeling of the NEXAFS F K‐edge spectra detected a change in the fluorine pattern with the increase of the F 2 treatment temperature. The presence of HF in fluorine gas was found to accelerate the fluorination process and cause a partial destruction of outer shells of the DWCNTs.
We propose a simple and effective way of creating pure dark superposition states. The generation of pure states is carried out by using bichromatic radiation with controllable polarization ellipticity. We derived analytic formulas for polarization elipticity to obtain pure dark states of different Zeeman sublevels of alkali atoms. Experimentally we accumulated ~60% of the atoms in the 0-0 dark state of the D1 line of Rb87
Aim. Production and purification of the recombinant histidine-tagged Y-box-binding protein 1 and study of its interaction with DNA, RNA and poly(ADP-ribose).

Methods.Ligationindependent cloning, PCR, Sanger sequencing, protein chromatography, polyacrylamide gel electrophoresis, and electrophoresis mobility shift assay.Results.cDNA coding for the YB-1 protein has a previously undocumented two single nucleotide polymorphisms.The expression construct for production of the his-tagged YB-1 protein was designed to simplify the purification procedure and an appropriate protocol for protein purification was developed.Using electrophoresis mobility shift assay, we have shown that poly(ADP-ribose) competes with a double-and single-stranded DNA and RNA for binding to purified recombinant his-tagged YB-1.

Conclusions.In the present work we developed and optimized the procedure of the recombinant YB-1 protein production and purification from bacterial cells.We found that poly(ADP-ribose) at high concentration is able to recruit YB-1 protein from the YB-1-DNA and YB-1-RNA complexes, suggesting a possible YB-1 involvement in DNA repair.
The work is devoted to the experimental study of the regularities of laminar-turbulent transition in supersonic boundary layers.

The experiments were carried out in the low-noise supersonic wind tunnel T-325 of ITAM SB RAS. The measurements were made by a constant-temperature hot-wire anemometer in the scanning mode. The procedure of decomposition of the fluctuations of the boundary layer into temperature and mass flux disturbances was carried out. The level of pulsations in the free flow of the test section of the T-325 wind tunnel was determined. The laminar-turbulent transition of two-dimensional supersonic boundary layer was experimentally investigated at Mach number M = 2 and 2.5. The levels of total temperature and mass flow pulsations were measured.

It was found that at the laminar-turbulent transition process the ratio of the mass flow and total temperature pulsations remains almost constant.
It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya).

Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck.

In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
The features of near-threshold mode of initiating by gas-tight piston and high- enthalpy gas flow was evaluated for a powder density explosive PETN. Both methods lead to the development of detonation in about 10 μs time. The synchrotron radiation diagnostics have shown that the initial stages of the process were significantly different, that diversity being caused by the influence of the gas flow in the pores of the charge. In this work, the effect of the gas flow on the mode of initiation was studied experimentally.
Nuclear magnetic resonance (NMR) has become a universal method for biochemical and biomedical studies, including metabolomics, proteomics, and magnetic resonance imaging (MRI). By increasing the signal of selected molecules, the hyperpolarization of nuclear spin has expanded the reach of NMR and MRI even further (e.g. hyperpolarized solid‐state NMR and metabolic imaging in vivo). Parahydrogen (pH 2 ) offers a fast and cost‐efficient way to achieve hyperpolarization, and the last decade has seen extensive advances, including the synthesis of new tracers, catalysts, and transfer methods. The portfolio of hyperpolarized molecules now includes amino acids, which are of great interest for many applications. Here, we provide an overview of the current literature and developments in the hyperpolarization of amino acids and peptides.
Whereas commercially available hematological analyzers measure volume of individual platelets, angle‐resolved light‐scattering provides unique ability to additionally measure their shape index. We utilized the scanning flow cytometer to measure light‐scattering profiles (LSPs) of individual platelets taken from 16 healthy donors and the solution of the inverse light‐scattering problem to retrieve the volume and shape index of each platelet. In normal conditions, the platelet shape index distribution (PSID) demonstrates three peaks, which relate to resting, partially activated, and fully activated platelets. We developed an algorithm, based on fitting PSID by a sum of three peak functions, to determine the percentage, mean platelet shape index, and distribution width of each platelet fraction. In total, this method gives eight additional parameters of platelet morphology and function to be used in clinical hematological analysis. We also stimulated the platelets with adenosine diphosphate (ADP) and measured the dependence of equilibrium PSID, including the total percentage of activated platelets, on ADP concentration. © 2016 International Society for Advancement of Cytometry
Gene expression plays an important role in the mechanisms of long-term potentiation (LTP), which is a widely accepted experimental model of synaptic plasticity. We have studied the expression of at least 50 genes that are transcriptionally regulated by p53, as well as other genes that are related to p53-dependent processes, in the early phase of LTP. Within 30 min after Schaffer collaterals (SC) tetanization, increases in the mRNA and protein levels of Bax, which are upregulated by p53, and a decrease in the mRNA and protein levels of Bcl2, which are downregulated by p53, were observed. The inhibition of Mdm2 by nutlin-3 increased the basal p53 protein level and rescued its tetanization-induced depletion, which suggested the involvement of Mdm2 in the control over p53 during LTP. Furthermore, nutlin-3 caused an increase in the basal expression of Bax and a decrease in the basal expression of Bcl2, whereas tetanization-induced changes in their expression were occluded. These results support the hypothesis that p53 may be involved in transcriptional regulation during the early phase of LTP. We hope that the presented data may aid in the understanding of the contribution of p53 and related genes in the processes that are associated with synaptic plasticity.
Background . Predominant use of the H1 and Gro1-4 genes of resistance to golden nematode (PGN) in potato breeding requires widening the gene pool of resistance to this pathogen.

Materials and methods . Thirty-four genotypes of wild potatoes from North and South Americas, 14 interspecific hybrids, and 10 Russian potato cultivars were studied for PGN resistance. Screening for resistance to PGN pathotype Ro1 and molecular screening for the presence of H1 and Gro1-4 gene markers were performed. Amplification products of the Gro1-4 gene marker were sequenced.

Results . Only seven among the studied 34 potato genotypes (two of S. brachystotrichum (Bitt.) Rydb., four of S. lesteri Hawkes et Hjerting, and one of S. kurtzianum Bitt. et Wittm.) were susceptible to PGN, while the rest demonstrated high or medium resistance. Molecular screening for the presence of H1 and Gro1-4 gene markers allowed us to identify Gro1-4 in 13 South American genotypes of S. alandiae Cárd., S. × doddsii Corr., S. kurtzianum , S. leptophyes Bitt., and S. yungasense Hawkes. The remaining 14 genotypes may supposedly contain resistance genes non-identical to H1 or Gro1-4 . Hybrids of S. tuberosum L. with medium-resistant wild accessions of S. kurtzianum , S. leptophyes , S. sparsipilum (Bitt.) Juz. et Buk., S. alandiae , and S. × doddsii inherited PGN resistance determined either by the Gro1-4 gene or genes non-identical to H1 or Gro1-4 . Sequencing a fragment of the Gro1-4 gene showed that changes in the structure of this fragment in orthologous genes did not affect the feature of resistance to PGN pathotype Ro1. Conclusion . For the first time, sources of resistance to PGN were found among the North American species S. brachystotrichum (k-23201) and S. lesteri (k-24475). Among the wild South American Solanum spp., sources of resistance determined by genes different from H1 or Gro1-4 were identified. Resistant interspecific hybrids can serve as donors of the Gro1-4 resistance gene or new resistance genes.
Recent findings indicate that the microbiome can have a significant impact on the development of lung cancer by inducing inflammatory responses, causing dysbiosis and generating genome damage. The aim of this study was to search for bacterial markers of squamous cell carcinoma (LUSC). In the study, the taxonomic composition of the sputum microbiome of 40 men with untreated LUSC was compared with 40 healthy controls. Next Generation sequencing of bacterial 16S rRNA genes was used to determine the taxonomic composition of the respiratory microbiome. There was no differences in alpha diversity between the LUSC and control groups. Meanwhile, differences in the structure of bacterial communities (β diversity) among patients and controls differed significantly in sputum samples (pseudo-F = 1.65; p = 0.026). Only Streptococcus , Bacillus , Gemella and Haemophilus were found to be significantly increased in patients with LUSC compared to the control subjects, while 19 bacterial genera were significantly reduced, indicating a decrease in beta diversity in the microbiome of patients with LUSC. From our study, Streptococcus ( Streptococcus agalactiae ) emerges as the most likely LUSC biomarker, but more research is needed to confirm this assumption.
Rare single nucleotide polymorphisms (SNPs) are likely to be a crucial genetic factor for human diseases, including cancer. rs78378222 is rare SNP in 3'-untranslated region (UTR) of TP53 gene leading to disturbance of 3'-end mRNA processing. The frequency of rs78378222 varies in several studied populations. The meta-analysis of 34 genome-wide association studies indicated that rs78378222 was significantly associated with an increased risk of cancer overall. Bioinformatic analysis indicates that somatic loss of the protective A allele of rs78378222 occurs in the tumor tissue of some malignant.

The goal of the current study is to document the rs78378222 prevalence and evaluate the copy loss status of the protective allele A in the tumor tissue of patients with diffuse large B-cell lymphoma (DLBCL).Total DNA was isolated from FFPE-samples and peripheral blood of patients with DLBCL and comparable in age and sex controls. rs78378222 genotyping was performed by the PCR-RFLP method using restriction endonuclease HindIII. Direct Sanger's sequencing was used to confirm the presence of C allele of the rs78378222. The search for TP53 gene mutations was carried out by Sanger's direct sequencing method, according to the IARC protocol.

The result of genotyping of 136 DNA samples from DLBCL tumor tissue suggested that frequency of the rs78378222 was 11/136 (8.1%). Rare allele C frequency was 11/272 (4.2%). A total of 5/11 DLBCL rs78378222 heterozygous samples had the heterozygosity loss in the TP53 gene. Only one of these cases was combined with TP53 gene mutations which have proven oncogenic potential-p.Arg196Gln, other four cases have not mutations in the coding regions of gene.At the stages of DLBCL initiation or progression a loss of the protective allele A of rs78378222 occurs. Further efforts are needed to study possible molecular mechanisms underlying somatic alterations in DLBCL in this region of the TP53 3'-UTR as well as functional studies to illustrate how the presents of rs78378222 may affect tumor progression of lymphoma.
This work presents result of visualisation of the characteristic combustion regimes of methane-air and syngas-air swirl-stabilized flames for an unconfined premixed burner (Re = 5000) and non-premixed combustion chamber (Re = 30000). Equivalence ratios were selected to have nearly equal values of the laminar flame propagation speed for the methane/air and syngas/air flames. Visualization for the premixed combustion for the model swirl burner revealed a similar shape of the flames for all mixtures. In contrast, during combustion of methane and syngas in the combustion chamber in the case of combustion in the combustion chamber, these differences in parameters cause completely visually diverse combustion modes.
Here, we introduce the idea of probabilities of line origins for alleles in general pedigrees as found in crosses between outbred lines. We also present software for calculating these probabilities. The proposed algorithm is based on the linear regression method of Haley, Knott and Elsen (1994) combined with the Markov chain Monte Carlo (MCMC) method for estimating quantitative trait locus coefficients used as regressors. We compared the relative precision of our method and the original method as proposed by Haley et al. (1994). The scenarios studied varied in the allelic distribution of marker alleles in parental lines and in the frequency of missing marker genotypes. We found that the MCMC method achieves a higher accuracy in all scenarios considered. The benefits of using MCMC approximation are substantial if the frequency of missing marker data is high or the number of marker alleles is low and the allelic frequency distribution is similar in both parental lines.
Methionine γ-lyase (MGL) catalyzes the γ-elimination of l-methionine and its derivatives as well as the β-elimination of l-cysteine and its analogs. These reactions yield α-keto acids and thiols. The mechanism of chemical conversion of amino acids includes numerous reaction intermediates. The detailed analysis of MGL interaction with glycine, l-alanine, l-norvaline, and l-cycloserine was performed by pre-steady-state stopped-flow kinetics. The structure of side chains of the amino acids is important both for their binding with enzyme and for the stability of the external aldimine and ketimine intermediates. X-ray structure of the MGL·l-cycloserine complex has been solved at 1.6 Å resolution. The structure models the ketimine intermediate of physiological reaction. The results elucidate the mechanisms of the intermediate interconversion at the stages of external aldimine and ketimine formation.
Aim: to evaluate the association of a complex of cardiovascular risk factors and genetic markers with the development of high albuminuria among patients with arterial hypertension in the population of Mountain Shoriya, taking into account ethnicity.

Materials and methods. A clinical epidemiological study of a compactly residing population in remote areas of Mountain Shoria was carried out. 1409 people were examined [901 people - representatives of the indigenous nationality (Shorians), 508 people - representatives of non-indigenous nationality (90% of them are Caucasians)]. Hypertension was diagnosed according to the National Guidelines of the Russian Society of Cardiology/the Russian Medical Society on Arterial Hypertension (2010). All patients underwent clinical, laboratory and instrumental investigation. To study the state of the kidneys, the concentration (the presence of elevated levels) of albumin (albuminuria) in the morning portion of urine by an immunoturbidimetric method was analyzed. Polymorphisms of genes ACE (I/D, rs4340), АGT (c.803T>C, rs699), AGTR1 (А1166С, rs5186), ADRB1 (с.145A>G, Ser49Gly, rs1801252), ADRA2B (I/D, rs28365031), MTHFR (c.677С>Т, Ala222Val, rs1801133) and NOS3 (VNTR, 4b/4a) were tested using PCR.

Results. In the group of shors with arterial hypertension, high albuminuria was associated with polymorphisms of the ACE genes (OR=2.05), ADRA2B (OR=6.00), elevated triglyceride level (OR=2.86), decreased index of cholesterol of high density lipoproteins (OR=5.57) and increased index of low density lipoproteins (OR=2.49); in the new population - with polymorphisms of the AGTR1 genes (OR=8.66), ADRA2B (OR=6.53), MTHFR (OR=7.16), obesity (OR=2.72), and abdominal obesity (OR=3.14). Conclusion. The primary predictors determining the development of high albuminuria among patients with arterial hypertension in both ethnic groups were genetic ones. In addition to them, non-genetic risk factors also contributed to the development of this organ damage to the kidneys: age and lipid metabolism disorders in representatives of indigenous nationality; age and abdominal obesity in the examined patients non-indigenous nationality.
Over the past two decades, the high energy physics community has been actively discussing and developing a number of post-LHC collider projects; however, none of them have been approved due to high costs and the uncertainty in post-LHC physics scenarios.There have been great expectations of rich new physics in the 0.1-1 TeV/c 2 mass region: the Higgs boson (one or several), supersymmetry, or perhaps new particles from the dark-matter family.It has been the general consensus that the best machine for the detailed study of new physics to be discovered at the LHC would be an energy-frontier linear e + e -collider.Physicists held their breath waiting for the results from the LHC.In summer 2012, two LHC detectors, ATLAS and CMS, announced the discovery of a Higgs boson with the mass of 126 GeV/c 2 -and (still) nothing else.The absence of new physics in the region below 1 TeV/c 2 has changed the post-LHC collider R&D priorities and triggered a zoo of project proposals for the precision study of the 126 GeV/c 2 Higgs boson, possibly with further upgrades to higher energies.This paper gives an overview of these projects;
Two Japanese sugar beet line with incomplete monogermity, TK-80-2BR2mm-CMS and its maintainer TK-80-2BR 2mm-O, were analyzed with a probe linked with a major gene of monogermity, M-m, for restriction fragment length polymorphism (RFLP). The relationship between monogermity and the RFLP pattern was suggested, although the ambiguous phenotypes were sometimes observed.
The B^0_s-\bar{B}^0_s oscillation frequency Delta m_s is measured with 36 pb^{-1} of data collected in pp collisions at \sqrt{s} = 7 TeV by the LHCb experiment at the Large Hadron Collider. A total of 1381 B^0_s -> D_s^- \pi^+ and \B^0_s -> D_s^- pi^+ pi^- pi^+ signal decays are reconstructed, with average decay time resolutions of 44 fs and 36 fs, respectively. An oscillation signal with a statistical significance of 4.6 sigma is observed. The measured oscillation frequency is Delta m_s = 17.63 \pm 0.11 (stat) \pm 0.02 (syst) ps^{-1}.
In the study of the reaction e+e−→ KSKL at the VEPP-2M e+e− collider with the SND detector

the nuclear interaction length of KL meson in NaI(Tl) has been measured. Its value is found to be 30–50 cm in the KL momentum range 0.11–0.48 GeV/c

The results are compared with the values used in the simulation programs GEANT4 and UNIMOD