The PCA-seq method applied to analyze of the dynamics of COVID-19 epidemic indicators

In time series analysis using the SSA method, a univariate series is converted into the multivariate one by shifts. The resulting trajectory matrix is subjected to principal component analysis (PCA). However, the principal components can also be computed using the PCA-Seq method if segments of the original series are selected as objects. The matrix of Euclidean distances between the objects can be obtained using any method, which offers additional opportunities for time series analysis compared to the conventional SSA. In this study, the PCA-Seq method was used to analyze the dynamics of COVID-19 epidemic indicators

The gene-expression profile of renal medulla in ISIAH rats with inherited stress-induced arterial hypertension

Metabolic pathways enriched with genes differentially expressed in ISIAH and WAG renal medulla. (XLS 41 kb

Evolution of spiral and scroll waves of excitation in a mathematical model of ischaemic border zone

Abnormal electrical activity from the boundaries of ischemic cardiac tissue is recognized as one of the major causes in generation of ischemia-reperfusion arrhythmias. Here we present theoretical analysis of the waves of electrical activity that can rise on the boundary of cardiac cell network upon its recovery from ischaemia-like conditions. The main factors included in our analysis are macroscopic gradients of the cell-to-cell coupling and cell excitability and microscopic heterogeneity of individual cells. The interplay between these factors allows one to explain how spirals form, drift together with the moving boundary, get transiently pinned to local inhomogeneities, and finally penetrate into the bulk of the well-coupled tissue where they reach macroscopic scale. The asymptotic theory of the drift of spiral and scroll waves based on response functions provides explanation of the drifts involved in this mechanism, with the exception of effects due to the discreteness of cardiac tissue. In particular, this asymptotic theory allows an extrapolation of 2D events into 3D, which has shown that cells within the border zone can give rise to 3D analogues of spirals, the scroll waves. When and if such scroll waves escape into a better coupled tissue, they are likely to collapse due to the positive filament tension. However, our simulations have shown that such collapse of newly generated scrolls is not inevitable and that under certain conditions filament tension becomes negative, leading to scroll filaments to expand and multiply leading to a fibrillation-like state within small areas of cardiac tissue.Comment: 26 pages, 13 figures, appendix and 2 movies, as accepted to PLoS ONE 2011/08/0

Starch phosphorylation associated SNPs found by genome-wide association studies in the potato (Solanum tuberosum L.)

Abstract Background The natural variation of starch phosphate content in potatoes has been previously reported. It is known that, in contrast to raw starch, commercially phosphorylated starch is more stable at high temperatures and shear rates and has higher water capacity. The genetic improvement of phosphate content in potato starch by selection or engineering would allow the production of phosphorylated starch in a natural, environmentally friendly way without chemicals. The aim of the current research is to identify genomic SNPs associated with starch phosphorylation by carrying out a genome-wide association study in potatoes. Results A total of 90 S. tuberosum L. varieties were used for phenotyping and genotyping. The phosphorus content of starch in 90 potato cultivars was measured and then statistically analysed. Principal component analysis (PCA) revealed that the third and eighth principal components appeared to be sensitive to variation in phosphorus content (p = 0.0005 and p = 0.002, respectively). PC3 showed the correlation of starch phosphorus content with allelic variations responsible for higher phosphorylation levels, found in four varieties. Similarly, PC8 indicated that hybrid 785/8–5 carried an allele associated with high phosphorus content, while the Impala and Red Scarlet varieties carried alleles for low phosphorus content. Genotyping was carried out using an Illumina 22 K SNP potato array. A total of 15,214 scorable SNPs (71.7% success rate) was revealed. GWAS mapping plots were obtained using TASSEL based on several statistical models, including general linear models (GLMs), with and without accounting for population structure, as well as MLM. A total of 17 significant SNPs was identified for phosphorus content in potato starch, 14 of which are assigned to 8 genomic regions on chromosomes 1, 4, 5, 7, 8, 10, and 11. Most of the SNPs identified belong to protein coding regions; however, their allelic variation was not associated with changes in protein structure or function. Conclusions A total of 8 novel genomic regions possibly associated with starch phosphorylation on potato chromosomes 1, 4, 5, 7, 8, 10, and 11 was revealed. Further validation of the SNPs identified and the analysis of the surrounding genomic regions for candidate genes will allow better understanding of starch phosphorylation biochemistry. The most indicative SNPs may be useful for developing diagnostic markers to accelerate the breeding of potatoes with predetermined levels of starch phosphorylation

Направленная асимметрия морфологических признаков в течение постнатального онтогенеза у полевки-экономки Microtus oeconomus Pall. (Rodentia, Cricetidae)

We analyzed Microtus oeconomus material collected for 25 years (1982–1992, 1994–2005, 2009, 2010). Directional asymmetry (DA) was demonstrated for teeth morphotypes, adrenal and kidney weights, and for length of the hind paw as well. DA may be formed both at early and later development stages and is not dependent on environmental factors and population density dynamics. Although each trait has its own dynamics DA in ontogeny, usually DA increases in the period of sexual maturation. Uncoordinated development of the sides in this period seems to associate with an increase in intensity of developmental processes. Our study argues that sexual dimorphism of continuous traits appears at the later developmental stages. This finding is consistent with Geodakian’s evolutionary theory of sex. Evolutionary significance of the DA is to increase both short-term individual fitness and long-term population adaptive capacity. Developmental approach to the study of morphological and functional asymmetries in animals opens new possibilities for the study of evolutionary processesПроанализирован материал по изменчивости билатеральных морфологических признаков полевки-экономки Microtus oeconomus, собранный в течение 25 лет (1982–1992, 1994–2005, 2009, 2010). Выявлена направленная асимметрия (НА) морфотипов коренных зубов, веса надпочечников и почек, а также длины задней лапы. Показано, что НА может формироваться как на ранних, так и на поздних стадиях онтогенеза и, по-видимому, имеет четкую генетическую детерминацию. Кроме того, НА каждого метрического признака имеет свою собственную онтогенетическую траекторию, которая не зависит от факторов среды и динамики численности популяции. В период полового созревания происходит нарастание НА всех метрических признаков, предположительно связанное с нарастанием напряженности процессов развития. Показано, что половой диморфизм НА формируется на поздних стадиях онтогенеза, что хорошо согласуется с эволюционной теорией пола В.А. Геодакяна. Эволюционное значение НА заключается в повышении адаптивных возможностей как отдельного организма, так и всей популяции. Онтогенетический подход к исследованию морфо- функциональных асимметрий у животных открывает новые возможности для исследования эволюционных процессо