SNOntology: Myriads of novel snornas or just a mirage?

<p>Abstract</p> <p>Background</p> <p>Small nucleolar RNAs (snoRNAs) are a large group of non-coding RNAs (ncRNAs) that mainly guide 2'-O-methylation (C/D RNAs) and pseudouridylation (H/ACA RNAs) of ribosomal RNAs. The pattern of rRNA modifications and the set of snoRNAs that guide these modifications are conserved in vertebrates. Nearly all snoRNA genes in vertebrates are localized in introns of other genes and are processed from pre-mRNAs. Thus, the same promoter is used for the transcription of snoRNAs and host genes.</p> <p>Results</p> <p>The series of studies by Dahai Zhu and coworkers on snoRNAs and their genes were critically considered. We present evidence that dozens of species-specific snoRNAs that they described in vertebrates are experimental artifacts resulting from the improper use of Northern hybridization. The snoRNA genes with putative intrinsic promoters that were supposed to be transcribed independently proved to contain numerous substitutions and are, most likely, pseudogenes. In some cases, they are localized within introns of overlooked host genes. Finally, an increased number of snoRNA genes in mammalian genomes described by Zhu and coworkers is also an artifact resulting from two mistakes. First, numerous mammalian snoRNA pseudogenes were considered as genes, whereas most of them are localized outside of host genes and contain substitutions that question their functionality. Second, Zhu and coworkers failed to identify many snoRNA genes in non-mammalian species. As an illustration, we present 1352 C/D snoRNA genes that we have identified and annotated in vertebrates.</p> <p>Conclusions</p> <p>Our results demonstrate that conclusions based only on databases with automatically annotated ncRNAs can be erroneous. Special investigations aimed to distinguish true RNA genes from their pseudogenes should be done. Zhu and coworkers, as well as most other groups studying vertebrate snoRNAs, give new names to newly described homologs of human snoRNAs, which significantly complicates comparison between different species. It seems necessary to develop a uniform nomenclature for homologs of human snoRNAs in other vertebrates, e.g., human gene names prefixed with several-letter code denoting the vertebrate species.</p

On spatial structure of the wave field in a vertical section of a deep water acoustic waveguide

The spatial structure of the wave field excited by a tonal point source in an underwater acoustic waveguide with random sound speed fluctuations is analyzed. This is done using an approach in which the field is approximated by a sum of components formed by contributions of narrow beams of rays. These components fluctuate less than the total field and, therefore, they are called stable. Each ot them can be isolated from the total field recorded by a long vertical antenna, using the coherent state expansion developed in quantum mechanics. An approximate analytical expression is obtained for the correlation matrix of the superposition of several stable components. The applicability of this equation is confirmed by the results of Monte Carlo simulation. The simulation has confirmed the theoretical prediction that nearly the same stable components can correspond to the sound speed fluctuations with completely different correlation functions

Refractive Errors in Children with Retinoblastoma

Purpose. Analysis of refractive errors’ frequency in children with retinoblastoma.Patients and Methods. A retrospective study included 57 children with retinoblastoma (31 male and 26 female) who received treatment in 2013–2017. The criteria for patient selection was the presence of mono- or bilateral retinoblastoma, as well as autorefractometry of both eyes before treatment. In all cases, the study was performed with cycloplegia. The parameters studied included gender, age at the time of the initial examination, visual acuity, spherical and cylindrical component of refraction, the axis of the cylinder.Results. Bilateral retinoblastoma was determined in 34 children (59.6 %), the average age of the patients was 18.0 ± 2.6 months. Monolateral retinoblastoma was detected in 23 patients (40.4 %), the average age at the time of check-up was 26.2 ± 3.1 months. In total, anisometropia of more than 2.0 diopters was detected in 14 patients (24.6 %), of which with monolateral RB in 6 patients (26.1 %) and in bilateral patients in 8 (23.5 %). In 26 cases (45.6 %) anisometropia was determined from 1.0 to 2.0 diopters, of which 41.1 % (n = 14) with bilateral lesion and 52.1 % (n = 12) with monolateral. The frequency of hyperopia over 3.0 diopters in the total cohort was 25.2 %, myopia 3.3 %. Significant differences (p = 0.025) were obtained by comparing the frequency of astigmatism determination of more than 1.0 D (39.6 % in the total cohort versus 13.0 % for healthy eyes). When analyzing the frequency of ametropia depending on age, a trend was observed (0.05 &lt; p &lt; 0.1) to reduce the frequency of hypermetropia and increase the frequency of astigmatism. Additionally, an analysis of the astigmatism’s frequency depending on the tumor localization was made. Patients with central or paracentral localization of the tumor lesion amounted to 69.4 % (n = 25), and from the peripheral — 30.6 % (n = 11) (p = 0.002).Conclusions. In this paper, we analyzed the frequency and nature of refractive errors in children with monolateral and bilateral retinoblastoma. The identified risk factors may affect the development of refractive amblyopia in children with retinoblastoma in more adulthood, which requires the development of an individual approach to the correction of refractive disorders taking into account the localization of tumor foci, the nature of the lesion and the individual characteristics of patients

LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria.

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