Optimization of a coronavirus genus recognition procedure based on the n-gene of prototypic strains

The article offers a solution to the problem of fast and efficient recognition of the coronavirus genus. For this purpose, the authors apply a virus genome targeting method based on the use of a sufficiently short and conserved N-gene of the nucleocapsid protein. Comparison of the codon frequency distributions in the N-gene of the analyzed genome and a set of 67 prototypical strains corresponding to the coronavirus subgenus allows us to recognize the genus of the coronavirus. This paper proposes optimization of the genus recognition of coronavirus by eliminating a significant number of codons from the 64 codons of the genetic code (26 in one case and 57 in the other). The authors achieved 100% genus recognition efficiency in a sample of 2,051 coronavirus genomes from the GenBank database with annotated subgenus in the optimized procedure. The authors also achieved 99% confidence when using the optimized coronavirus genus recognition procedure in a total sample of 3,242 genomes

Profile-Statistical Periodicity of DNA Coding Regions

Novel methods for identifying a new type of DNA latent periodicity, called latent profile periodicity or latent profility, are used to search for periodic structures in genes. These methods reveal two distinct levels of organization of genetic information encoding. It is shown that latent profility in genes may correlate with specific structural features of their encoded proteins

Study of the multivariable adaptative spectrofilter with forgetting factor

After a brief survey of noise cancelling using the noise references principle, we analyse the influence of estimation errors, of the varions filter components, when a finite integration window equivalent length is used, with a forgetting factor . This one is needful to most real processings . The error power is expressed according to the various parametees . Then we observe that the output signal to noise ratio is solely fonction of the forgetting factor value (lenght of the integration window) and the number of the noise references used. We settle this theorically and we verify our results with simulations . The efficiency of the process is considered and we provide noise references selection criteria .Après avoir rappelé brièvement le principe de la soustraction de bruit avec références bruit seul, nous analysons l'influence des erreurs d'estimation des différentes composantes du filtre, sur une fenêtre d'intégration de longueur équivalente finie, lorsqu'un facteur d'oubli est employé . Ce dernier est nécessaire pour le traitement de la plupart des signaux réels . La puissance d'erreur en sortie de traitement est exprimée en fonction des différents paramètres et, nous montrons que le rapport signal à bruit en sortie de traitement est uniquement fonction de la valeur du facteur d'oubli (c'est-à-dire de la longueur équivalente de la fenêtre d'intégration) et du nombre de références-bruit utilisées . Nous déterminons ceci théoriquement et le vérifions par des simulations dont nous présentons les résultats . Le problème de l'efficacité du traitement est abordée et, nous fournissons des critères de sélection des références bruit

Information decomposition of symbolic sequences

We developed a non-parametric method of Information Decomposition (ID) of a content of any symbolical sequence. The method is based on the calculation of Shannon mutual information between analyzed and artificial symbolical sequences, and allows the revealing of latent periodicity in any symbolical sequence. We show the stability of the ID method in the case of a large number of random letter changes in an analyzed symbolic sequence. We demonstrate the possibilities of the method, analyzing both poems, and DNA and protein sequences. In DNA and protein sequences we show the existence of many DNA and amino acid sequences with different types and lengths of latent periodicity. The possible origin of latent periodicity for different symbolical sequences is discussed.Comment: 18 pages, 8 figure

Сравнительный анализ асептического введения и стабилизации in vitro разных типов эксплантов ясеня обыкновенного

В настоящей статье впервые приведены результаты применения 24–эпибрассинолида на этапе стабилизации in vitro регенерантов ясеня обыкновенного Fraxinus excelsior L., семенного происхождения. В работе использовали семена, собранные в 2016 году в Гомельской и Гродненской областях Республики Беларусь. Показано, что наиболее подходящим типом первичного экспланта ясеня обыкновенного для асептического введения в культуру in vitro являются изолированные зародыши. Для успешного асептического введения in vitro от 57–100% изолированных зародышей ясеня обыкновенного рекомендуется питательная, агаризованная сре-да Мурасиге и Скуга половинного состава без фитогормонов, с добавлением 20 г/л сахарозы, 9 г/л агар–агара, при рН=5,6. Для успешной стабилизации in vitro регенерантов ясеня обыкновенного можно рекомендовать питательную, агаризованную среду Андерсона, дополненную 1 мг/л зеати-на и 0,75 мг/л 24–эпибрассинолида, при этом у всех регенерантов ясеня обыкновенного формируются корни в количестве от 1–3 и длиной от 0,6–6,0 см, в зависимости от генотипа. For the first time in the world the results of application of 24–epibrassinolid in a stage of stabilization in vitro of european ash (Fraxinus excelsior L.) regenerants of seed origin are given in the present article. In work there are used the seeds collected in 2016 in the Gomel and Grodno regions of the Republic of Belarus. It is shown that the most suitable type of primary explants of european ash for aseptic introduction in vitro are the isolated germs. For successful aseptic in vitro introduction in amount of 57–100% of the european ash isolated germs is recommended the nutrient, agarized medium of half Murasige and Skoog’s compound without phytohormones, with addition of 20 g per liter of sucrose, of 9 g per liter of agar–agar, and of рН=5,6. For successful in vitro stabilization of the european ash regenerants is recommended the nutrient, agarized Anderson’s medium added with 1 mg per liter of zeatin and of 0,75 mg per liter of 24–epibrassinolid. At the same time, all of the european ash regenerants depending on a genotype, are formed roots in quantity from 1–3 and from 0,6–6,0 cm long

Plastid division

This review considers the nature of the plastid division machinery that enables binary fission of plastids, from a cell biology perspective and considers how the cell might control aspects of plastid population control and segregation during plant development

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Coding Structure for the ORF1ab, S, M and N Coronavirus Genes

Spectral-statistical approach was applied to comparative analysis of coronavirus genomes from the four genus Alphacoronavirus, Betacoronavirus (including new SARS-CoV-2 virus), Gammacoronavirus and Deltacoronavirus. This analysis was done from the point of view of 3-regularity and latent triplet profile periodicity existence in the coding sequences of four structural genes: ORF1ab encoding transcriptase; S-gene of glycoprotein forming spikes; M-gene of membrane protein; N-gene of nucleoprotein. A whole number of the genomes analyzed was equal to 3410. Gene numbers in each of the four groups in the study respectively were the same. In the result, practically, in the CDSs of all analyzed genes of ORF1ab, S and N the latent profile triplet periodicity was revealed and high value of 3-regularity index, being a quality estimate of coding triplet structure conservation, was determined. On the contrary, for coding structure of M-genes a tendency was revealed to diffuse up to homogeneity for 60% of the genes in the genomes of alphacoronaviruses analyzed and for 67% of the genes of the gammacoronaviruses. Tendency of the such structure diffusion, being accompanied by decrease of 3-regularity index average value in comparison with other genes, while the triplet profile periodicity remains saved, was also noted for M-genes of SARS-CoV-2 viruses. Probably, this tendency reflects a significance of M-genes variability in coronavirus adaptation to the novel hosts of genus. Analysis of 3- profile periodicity matrices of the four groups of SARS-CoV-2 genes considered in the work, for the viruses isolated in Europe, Asia and USA, did not revealed their significant difference, that is allowing to propose a single source of this virus propagation