Composition and Dynamics of H1N1 and H7N9 Influenza A Virus Quasispecies in a Co-infected Patient Analyzed by Single Molecule Sequencing Technology

A human co-infected with H1N1 and H7N9 subtypes influenza A virus (IAV) causes a complex infectious disease. The identification of molecular-level variations in composition and dynamics of IAV quasispecies will help to understand the pathogenesis and provide guidance for precision medicine treatment. In this study, using single-molecule real-time sequencing (SMRT) technology, we successfully acquired full-length IAV genomic sequences and quantified their genotypes abundance in serial samples from an 81-year-old male co-infected with H1N1 and H7N9 subtypes IAV. A total of 26 high diversity nucleotide loci was detected, in which the A-G base transversion was the most abundant substitution type (67 and 64%, in H1N1 and H7N9, respectively). Seven significant amino acid variations were detected, such as NA:H275Y and HA: R222K in H1N1 as well as PB2:E627K and NA: K432E in H7N9, which are related to viral drug-resistance or mammalian adaptation. Furtherly, we retrieved 25 H1N1 and 22 H7N9 genomic segment haplotypes from the eight samples based on combining high-diversity nucleotide loci, which provided a more concise overview of viral quasispecies composition and dynamics. Our approach promotes the popularization of viral quasispecies analysis in a complex infectious disease, which will boost the understanding of viral infections, pathogenesis, evolution, and precision medicine.

Analysis of changes occurring in Codon Positions due to mutations through the cellular automata transition rules

Variation in the nucleotides of a codon may cause variations in the evolutionary patterns of a DNA or amino acid sequence. To address the capability of each position of a codon to have non-synonymous mutations, the concept of degree of mutation has been introduced. The degree of mutation of a particular position of codon defines the number of non-synonymous mutations occurring for the substitution of nucleotides at each position of a codon, when other two positions of that codon remain unaltered. A Cellular Automaton (CA), is used as a tool to model the mutations of any one of the four DNA bases A, C, T and G at a time where the DNA bases correspond to the states of the CA cells. Point mutation (substitution type) of a codon which characterizes changes in the amino acids, have been associated with local transition rules of a CA. Though there can be transitions of a 4-state CA with 3-neighbourhood cells, here it has been possible to represent all possible point mutations of a codon in terms of combinations of 16 local transition functions of the CA. Further these rules are divided into 4 classes of equivalence. Also, according to the nature of mutations, the 16 local CA rules of substitutions are classified into 3 sets namely, ‘No Mutation’, ‘Transition’ and ‘Transversion’. The experiment has been carried out with three sets of single nucleotide variations(SNVs) of three different viruses but the symptoms of the diseases caused by them are to some extent similar to each other. They are SARS-CoV-1, SARS-CoV-2 and H1N1 Type A viruses. The aim is to understand the impact of nucleotide substitutions at different positions of a codon with respect to a particular disease phenotype.

Development and Research of Copper Covering for Intensification of Cold Stamping of Products from Stainless Steels

The copper covering put in fused salts of chlorides at temperature of 450-500cC and preventing scuffs on the surface of steel of type 12X18H10T at cold stamping of case products and fixture was investigated. Metallurgical surveys have shown: 1) except cover zone and zone of base metal there is also transition zone, representing substitution type of solution; 2) in the course of application there is superficial alloying, due to penetration of atoms of copper deep into metal and diffusions of doping steel elements in coating material under the influence of melts's high temperature. The schedule of change of concentration of copper in diffusion zone allows to conclude that the copper covering consists not of pure copper, and that the alloy contains only 94% of copper; other 6% represent the chrome and the titanium diffusing in copper covering. It is established also that, despite strong cohesion with basis, the covering is completely removed from surface of the stamping details being dissolved in standard sulphuric acid solution.

Interaction of Components in the Lu-Ag-Si System at 500 ºC

Isothermal section of the Lu-Ag-Si system at 500ºC was studied by means of X-ray powder diffraction, microstructure and EDX-analyses in the whole concentration range. The existence of earlier reported binary compounds LuAg4, LuAg2, LuAg and LuSi2, LuSi, Lu5Si3, Lu5Si4 was confirmed. New binary compound Lu3Si5 (own str. type) was found. Almost none of the binary silicides dissolve more than 5 at.% of third component. The exception is the existence of the substitution type solid solutions based on LuAg2 (MoSi2-type structure), which dissolves up to 20 at.% Si, as well as on Lu5Si3 (Mn5Si3-type structure), which dissolves up to 15 at.% Ag. The crystal structure of the LuSi compound was redetermined by X-ray single crystal diffraction (TlI-type, space group Cmcm, a = 4.1493(3), b = 10.2641(7), c = 3.7518(2) Å, R = 0.0173, wR = 0.0415 for 173 independent reflections). No ternary compound is observed in the Lu-Ag-Si system.

The Focal Attention Window Size Explains Letter Substitution Errors in Reading

Acquired Neglect Dyslexia is often associated with right-hemisphere brain damage and is mainly characterized by omissions and substitutions in reading single words. Martelli et al. proposed in 2011 that these two types of error are due to different mechanisms. Omissions should depend on neglect plus an oculomotor deficit, whilst substitutions on the difficulty with which the letters are perceptually segregated from each other (i.e., crowding phenomenon). In this study, we hypothesized that a deficit of focal attention could determine a pathological crowding effect, leading to imprecise letter identification and consequently substitution errors. In Experiment 1, three brain-damaged patients, suffering from peripheral dyslexia, mainly characterized by substitutions, underwent an assessment of error distribution in reading pseudowords and a T detection task as a function of cue size and timing, in order to measure focal attention. Each patient, when compared to a control group, showed a deficit in adjusting the attentional focus. In Experiment 2, a group of 17 right-brain-damaged patients were asked to perform the focal attention task and to read single words and pseudowords as a function of inter-letter spacing. The results allowed us to confirm a more general association between substitution-type reading errors and the performance in the focal attention task.

Predictable Site-Selective Functionalization: Promoter Group Assisted para-Halogenation of N-Substituted (Hetero)Aromatics under Metal-Free Condition

Herein, regioselective para-C-H halogenation of N-pyrimidyl (hetero)aromatics through SEAr (Electrophilic aromatic substitution) type reaction is disclosed. SEAr type reaction has been utilized for the C5-bromination of indolines (para-selective) with N-bromosuccinimide...

Dynamic response of RNA editing to temperature in grape by RNA deep sequencing

RNA editing is a post-transcriptional process of modifying genetic information on RNA molecules, which provides cells an additional level of gene expression regulation. Unlike mammals, in land plants, RNA editing converts C-to-U residues in organelles. However, its potential roles in response to different stressors (heat, salt, and so on) remains unclear. Grape is one of the most popular and economically important fruits in the world, and its production, like other crops, must deal with abiotic and biotic stresses, which cause reductions in yield and fruit quality. In our study, we tested the influence of the environmental factor temperature on RNA editing process in the whole mRNA from grape organelle. In total, we identified 122 and 627 RNA editing sites in chloroplast and mitochondria respectively with the average editing efficiency nearly ~ 60%. The analyses revealed that number of non-synonymous editing sites were higher than that of synonymous editing sites, and the amino acid substitution type tends to be hydrophobic. Additionally, the overall editing level decreased with the temperature rises, especially for several gene transcripts in chloroplast and mitochondria (matK, ndhB, etc.). We also found that the expression level of most PPR genes decreased with the temperature rises, which may contribute to the decline of RNA editing efficiency at high temperature. Our findings suggested that the RNA editing events were very sensitive to heat stress; the changes of amino acid in RNA editing genes may contribute to the stress adaption for grape.

Bivariate Software Reliability Growth Models under Budget Constraint for Development Management

Software reliability growth is observed by investing not only the testing-time but also the testing-effort in the testing-phase of software development process. If the testing-time (testing-effort) is reduced to some extent, it is possible to observe the software reliability growth by investing the amount of testing-effort (testing-time) which can compensate the insufficiency of the testing-time (testing-effort). However, most of the existing software reliability growth models (SRGMs) are constructed as univariate models and the substitutability between the testing-time and testing-effort is not considered. Additionally, it is necessary to remove many faults efficiently within the budget. In this paper, we develop bivariate Weibull type SRGMs under budget constraint based on the Cobb-Douglas type and CES (constant elasticity of substitution) type testing-time functions. Simultaneously, we evaluate the substitutability between the testing-time and testing-effort factors which are software reliability growth factors. Finally, we conduct the sensitivity analysis and show numerical examples by using actual data sets.