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Bick J.,Yale University | Naumova O.,Yale University | Naumova O.,Vavilov Institute of General Genetics | Hunter S.,Yale University | And 8 more authors.
Development and Psychopathology

In recent years, translational research involving humans and animals has uncovered biological and physiological pathways that explain associations between early adverse circumstances and long-term mental and physical health outcomes. In this article, we summarize the human and animal literature demonstrating that epigenetic alterations in key biological systems, the hypothalamus-pituitary-adrenal axis and immune system, may underlie such disparities. We review evidence suggesting that changes in DNA methylation profiles of the genome may be responsible for the alterations in hypothalamus-pituitary-adrenal axis and immune system trajectories. Using some preliminary data, we demonstrate how explorations of genome-wide and candidate-gene DNA methylation profiles may inform hypotheses and guide future research efforts in these areas. We conclude our article by discussing the many important future directions, merging perspectives from developmental psychology, molecular genetics, neuroendocrinology, and immunology, that are essential for furthering our understanding of how early adverse circumstances may shape developmental trajectories, particularly in the areas of stress reactivity and physical or mental health. © Cambridge University Press 2012. Source

Mcdonald H.,London School of Hygiene and Tropical Medicine | Borinskya S.,Vavilov Institute of General Genetics | Kiryanov N.,Izhevsk State Medical Academy | Gil A.,London School of Hygiene and Tropical Medicine | And 3 more authors.

Aims: To assess the performance of a range of biomarkers of alcohol consumption in a heavy-drinking population of working-aged Russian men. Design: Cross-sectional study of men originally sampled at random from a population register. Setting: Izhevsk, a Russian city with a population of 650000 people. Participants: A total of 1023 men aged 27-59 years living in Izhevsk who took part in a health check examination in 2008-2009. Measurements: Self-reported alcohol consumption, hazardous drinking behaviours, socio-economic position, anthropometric measurements plus blood levels of alcohol biomarkers [carbohydrate-deficient transferrin (CDT, gamma-glutamyl transferase (GGT), alanine aminotransferase (ALT), aspartate aminotransferase (AST) and mean cell volume of erythrocytes (MCV)] and hepatitis B and C status. Findings: In the year before interview there was a high prevalence of high-risk alcohol consumption indicated by consumption of non-beverage alcohols (5%), problem drinking behaviours (4.4%) and alcohol consumption exceeding an average 40g per day (12.6%). All biomarkers were associated strongly with total beverage alcohol consumption even after adjustment for confounders. CDT performed best as an alcohol biomarker, with a sensitivity of 67% and specificity of 71% for detecting an average consumption of more than 40g per day versus less. For all biomarkers sensitivity was considerably lower than specificity. Hazardous drinking patterns per se were not well detected by any of the biomarkers, all with sensitivity below 60%. Conclusions: In a Russian population with high levels of alcohol consumption, carbohydrate-deficient transferrin (CDT) might be the most sensitive and specific biomarker for detecting ethanol consumption above 40g/day. A biomarker reflecting hazardous drinking patterns has yet to be established. © 2013 Society for the Study of Addiction. Source

Dragovich B.,Institute of Physics | Dragovich A.,Vavilov Institute of General Genetics
Computer Journal

This paper presents the foundations of p-adic modelling in genomics. Considering nucleotides, codons, DNA and RNA sequences, amino acids and proteins as information systems, we have formulated the corresponding p-adic formalisms for their investigations. Each of these systems has its characteristic prime number used for construction of the related information space. Relevance of this approach is illustrated by some examples. In particular, it is shown that degeneration of the genetic code is a p-adic phenomenon. We have also put a forward a hypothesis on the evolution of the genetic code assuming that primitive code was based on single nucleotides and chronologically first four amino acids. This formalism of p-adic genomic information systems can be implemented in computer programs and applied to various concrete cases. © The Author 2007. Published by Oxford University Press on behalf of The British Computer Society. All rights reserved. Source

Tuzhikov A.,University of Miami | Tuzhikov A.,Institute for Information Transmission Problems | Panchin A.,Institute for Information Transmission Problems | Shestopalov V.I.,University of Miami | Shestopalov V.I.,Vavilov Institute of General Genetics

Pyrosequencing of 16S ribosomal RNA (rRNA) genes has become the gold standard in human microbiome studies. Te routine task of taxonomic classification using 16S rRNA reads is commonly performed by the Ribosomal Database Project (RDP) II Classifier, a robust tool that relies on a set of well-characterized reference sequences. However, the RDP II Classifier may be unable to classify a significant part of the data set due to the absence of proper reference sequences. Te taxonomic classification for some unclassified sequences might still be performed using BLAST searches against large and frequently updated nucleotide databases. Here we introduce TUIT (Taxonomic Unit Identification Tool)-an efficient open source and platform-independent application that can perform taxonomic classification on its own or can be used in combination with the RDP II Classifier to maximize the taxonomic identification rate. Using a set of simulated DNA sequences, we demonstrate that the algorithm performs taxonomic classification with high specificity for sequences as short as 125 base pairs. TUIT is applicable for 16S rRNA gene sequence classifications; however, it is not restricted to 16S rRNA sequences. In addition, TUIT may be used as a complementary tool for effective taxonomic classification of nucleotide sequences generated by many current platforms, such as Roche 454 and Illumina. Source

Variability at the locus of major histocompatibility complex MHC-I A1 in 20 populations of pink salmon Oncorhynchus gorbuscha from the five major geographical regions of the Russian Far East was studied. Indices of genetic differentiation at all levels of the hierarchy were unexpectedly high and comparable with the corresponding estimates in related species of Pacific salmon. The data obtained allow us to revise the existing hypotheses concerning intraspecific structure of pink salmon, in particular, to reject the "fluctuating stock" hypothesis. Good resolution of the detected marker will find application in the problems of identification of populations in mixed catches. © 2012 Pleiades Publishing, Ltd. Source

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