GC₃ Biology in Eukaryotes and Prokaryotes

We describe the distribution of Guanine and Cytosine (GC) content in the third codon position (GC3) distributions in different species, analyze evolutionary trends and discuss differences between genes and organisms with distinct GC3 levels. We scrutinize previously published theoretical frameworks and construct a unified view of GC3 biology in eukaryotes and prokaryotes

Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa

Background The methylation of cytosines at CpG dinucleotides, which plays an important role in gene expression regulation, is one of the most studied epigenetic modifications. Thus far, the detection of DNA methylation has been determined mostly by experimental methods, which are not only prone to bench effects and artifacts but are also time-consuming, expensive, and cannot be easily scaled up to many samples. It is therefore useful to develop computational prediction methods for DNA methylation. Our previous studies highlighted the existence of correlations between the GC content of the third codon position (GC3), methylation, and gene expression. We thus designed a model to predict methylation in Oryza sativa based on genomic sequence features and gene expression data. Results We first derive equations to describe the relationship between gene methylation levels, GC3, expression, length, and other gene compositional features. We next assess gene compositional features involving sixmers and their association with methylation levels and other gene level properties. By applying our sixmer-based approach on rice gene expression data we show that it can accurately predict methylation (Pearson’s correlation coefficient r = 0.79) for the majority (79%) of the genes. Matlab code with our model is included. Conclusions Gene expression variation can be used as predictors of gene methylation levels

Evaluation of codon biology in citrus and poncirus trifoliata based on genomic features and frame corrected expressed sequence tags

Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of Citrus species and P. trifoliata. The present study postulates a large repertoire of a set of optimal codons for the Citrus genus and P. trifoliata and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in Citrus and P. trifoliata. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (~10.96%) of the recorded variance. In all analysed species, except P. trifoliata, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in Citrus species and P. trifoliata. Our present analysis postulates compositional constraints in Citrus species and P. trifoliata and plausible role of the stress with GC3 and coevolution pattern of amino acid. © The Author 2012

Predicion of charge separation in GaAs/AlAs cylindrical Russian Doll nanostructures

We have contrasted the quantum confinement of (i) multiple quantum wells of flat GaAs and AlAs layers, i.e. (\GaAs)_{m}/(\AlAs)_n/(\GaAs)_p/(\AlAs)_q, with (ii) ``cylindrical Russian Dolls'' -- an equivalent sequence of wells and barriers arranged as concentric wires. Using a pseudopotential plane-wave calculation, we identified theoretically a set of numbers ($m,n,p$ and $q$) such that charge separation can exist in ``cylindrical Russian Dolls'': the CBM is localized in the inner GaAs layer, while the VBM is localized in the outer GaAs layer.Comment: latex, 8 page

COVID-19-associated coagulopathy in children and adolescents

The pandemic of the new coronavirus infection COVID-19 in 2020 has become the main health problem across the globe. A special characteristic of the SARSCoV-2 virus is tropism to the vascular endothelium with the  development of endotheliitis, which entails a number of typical disorders of the blood coagulation system: coagulopathy with increased thrombin generation, D-dimer, decreased fibrinolysis and prolonged prothrombin time. The coagulation disorder in COVID-19 is called thromboinflammation. Hyperinflammation, increased blood levels of von Willebrand factor, coagulation factor VIII, neutrophil extracellular traps, platelet activation, microvesicles play a significant role in the pathogenesis of hypercoagulation in COVID-19. To date, it is known that cases of COVID-19 in children and adolescents constitute a small part of the total number of patients with diagnosed COVID-19, and disorders of the blood coagulation system are similar to those in adults. The degree of hypercoagulable syndrome and the risk of thrombosis depend on the severity of COVID-19. And for children they are most expressed with the development of a hyperinflammatory immune response, called multisystem inflammatory syndrome. At the same time, clinical studies of the pathogenesis of COVID-19 in adults and children and the search for optimal methods of therapy for thrombus inflammation, which underlies the pathogenesis of COVID-19, continue

A Case of Successful Medical Treatment of Ventricular Tachycardia in a Patient With Ischemic Heart Disease and Heart Failure

The pathogenetic mechanisms of arrhythmias, including  high-grade ventricular  arrhythmias (including non-sustained ventricular  tachycardia),  in patients with coronary  heart disease may be different. Therefore, the characteristics  of ventricular arrhythmias must be considered  based on the totality of data, taking  into account all the available features. The importance  of a personalized approach  to the management of a patient with coronary  heart disease who had extensive myocardial  infarction 18.5 years ago,  followed  by mammary  coronary  artery bypass  grafting, aneurysmectomy and the development of heart failure with a low ejection fraction, in whom ventricular arrhythmias occurred against the background of a stable course of coronary disease , but after emotional stress, is reflected in this work. An extended examination, as well as a detailed study of the nature of ventricular arrhythmias, made it possible  to determine  the main provoking factor and select an individualized pathogenetic treatment with a good  antiarrhythmic result that persists for several years of observation.  Conducting mental tests and psychological questioning can be recommended for patients with coronary  heart disease  and  chronic  heart failure as an additional  examination to assess  the contribution  of the psycho-emotional factor  to arrhythmogenesis after excluding the ischemic and sympathetic  nature of ventricular ectopia. It is incorrect to consider that all ventricular arrhythmias  in patients with coronary heart disease are ischemic in nature, and in some clinical situations this statement is even erroneous

THE PROCESS APPROACH TO EMPLOYEE ENGAGEMENT IN AN ORGANIZATION

It is proposed the view on engagement in an organization as engagement in the processes taking place in an organization. The authors describe Engagement in an organization Questionnaire development and results of validation and reliability control. The sample is consists of 84 employees.Предлагается взгляд на вовлеченность в организацию как вовлеченность сотрудника в процессы, протекающие в организации. Описывается путь разработки методики «Вовлеченность в организацию », а также результаты ее проверки на валидность и надежность на выборке из 84 человек

Theory of anyon excitons: Relation to excitons of nu=1/3 and nu=2/3 incompressible liquids

Elementary excitations of incompressible quantum liquids (IQL's) are anyons, i.e., quasiparticles carrying fractional charges and obeying fractional statistics. To find out how the properties of these quasiparticles manifest themselves in the optical spectra, we have developed the anyon exciton model (AEM) and compared the results with the finite-size data for excitons of nu=1/3 and nu=2/3 IQL's. The model considers an exciton as a neutral composite consisting of three quasielectrons and a single hole. The AEM works well when the separation between electron and hole confinement planes, h, is larger than the magnetic length l. In the framework of the AEM an exciton possesses momentum k and two internal quantum numbers, one of which can be chosen as the angular momentum, L, of the k=0 state. Existence of the internal degrees of freedom results in the multiple branch energy spectrum, crater-like electron density shape and 120 degrees density correlations for k=0 excitons, and the splitting of the electron shell into bunches for non-zero k excitons. For h larger than 2l the bottom states obey the superselection rule L=3m (m are integers starting from 2), all of them are hard core states. For h nearly 2l there is one-to-one correspondence between the low-energy spectra found for the AEM and the many- electron exciton spectra of the nu=2/3 IQL, whereas some states are absent from the many-electron spectra of the nu=1/3 IQL. We argue that this striking difference in the spectra originates from the different populational statistics of the quasielectrons of charge conjugate IQL's and show that the proper account of the statistical requirements eliminates excessive states from the spectrum. Apparently, this phenomenon is the first manifestation of the exclusion statistics in the anyon bound states.Comment: 26 pages with 9 figures, typos correcte

Theory of Photoluminescence of the ν=1\nu=1 Quantum Hall State: Excitons, Spin-Waves and Spin-Textures

We study the theory of intrinsic photoluminescence of two-dimensional electron systems in the vicinity of the $\nu=1$ quantum Hall state. We focus predominantly on the recombination of a band of initial ``excitonic states'' that are the low-lying energy states of our model at $\nu=1$. It is shown that the recombination of excitonic states can account for recent observations of the polarization-resolved spectra of a high-mobility GaAs quantum well. The asymmetric broadening of the spectral line in the $\sigma_-$ polarization is explained to be the result of the ``shake-up'' of spin-waves upon radiative recombination of excitonic states. We derive line shapes for the recombination of excitonic states in the presence of long-range disorder that compare favourably with the experimental observations. We also discuss the stabilities and recombination spectra of other (``charged'') initial states of our model. An additional high-energy line observed in experiment is shown to be consistent with the recombination of a positively-charged state. The recombination spectrum of a negatively-charged initial state, predicted by our model but not observed in the present experiments, is shown to provide a direct measure of the formation energy of the smallest ``charged spin-texture'' of the $\nu=1$ state.Comment: 23 pages, 7 postscript figures included. Revtex with epsf.tex and multicol.sty. The revised version contains slightly improved numerical results and a few additional discussions of the result

Comprehensive analysis of the base composition around the transcription start site in Metazoa

BACKGROUND: The transcription start site of a metazoan gene remains poorly understood, mostly because there is no clear signal present in all genes. Now that several sequenced metazoan genomes have been annotated, we have been able to compare the base composition around the transcription start site for all annotated genes across multiple genomes. RESULTS: The most prominent feature in the base compositions is a significant local variation in G+C content over a large region around the transcription start site. The change is present in all animal phyla but the extent of variation is different between distinct classes of vertebrates, and the shape of the variation is completely different between vertebrates and arthropods. Furthermore, the height of the variation correlates with CpG frequencies in vertebrates but not in invertebrates and it also correlates with gene expression, especially in mammals. We also detect GC and AT skews in all clades (where %G is not equal to %C or %A is not equal to %T respectively) but these occur in a more confined region around the transcription start site and in the coding region. CONCLUSIONS: The dramatic changes in nucleotide composition in humans are a consequence of CpG nucleotide frequencies and of gene expression, the changes in Fugu could point to primordial CpG islands, and the changes in the fly are of a totally different kind and unrelated to dinucleotide frequencies