Applying negative rule mining to improve genome annotation

<p>Abstract</p> <p>Background</p> <p>Unsupervised annotation of proteins by software pipelines suffers from very high error rates. Spurious functional assignments are usually caused by unwarranted homology-based transfer of information from existing database entries to the new target sequences. We have previously demonstrated that data mining in large sequence annotation databanks can help identify annotation items that are strongly associated with each other, and that exceptions from strong positive association rules often point to potential annotation errors. Here we investigate the applicability of negative association rule mining to revealing erroneously assigned annotation items.</p> <p>Results</p> <p>Almost all exceptions from strong negative association rules are connected to at least one wrong attribute in the feature combination making up the rule. The fraction of annotation features flagged by this approach as suspicious is strongly enriched in errors and constitutes about 0.6% of the whole body of the similarity-transferred annotation in the PEDANT genome database. Positive rule mining does not identify two thirds of these errors. The approach based on exceptions from negative rules is much more specific than positive rule mining, but its coverage is significantly lower.</p> <p>Conclusion</p> <p>Mining of both negative and positive association rules is a potent tool for finding significant trends in protein annotation and flagging doubtful features for further inspection.</p

Asymmetric and non-uniform evolution of recently duplicated human genes

<p>Abstract</p> <p>Background</p> <p>Gene duplications are a source of new genes and protein functions. The innovative role of duplication events makes families of paralogous genes an interesting target for studies in evolutionary biology. Here we study global trends in the evolution of human genes that resulted from recent duplications.</p> <p>Results</p> <p>The pressure of negative selection is weaker during a short time immediately after a duplication event. Roughly one fifth of genes in paralogous gene families are evolving asymmetrically: one of the proteins encoded by two closest paralogs accumulates amino acid substitutions significantly faster than its partner. This asymmetry cannot be explained by differences in gene expression levels. In asymmetric gene pairs the number of deleterious mutations is increased in one copy, while decreased in the other copy as compared to genes constituting non-asymmetrically evolving pairs. The asymmetry in the rate of synonymous substitutions is much weaker and not significant.</p> <p>Conclusions</p> <p>The increase of negative selection pressure over time after a duplication event seems to be a major trend in the evolution of human paralogous gene families. The observed asymmetry in the evolution of paralogous genes shows that in many cases one of two gene copies remains practically unchanged, while the other accumulates functional mutations. This supports the hypothesis that slowly evolving gene copies preserve their original functions, while fast evolving copies obtain new specificities or functions.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Igor Rogozin (nominated by Dr. Arcady Mushegian), Dr. Fyodor Kondrashov, and Dr. Sergei Maslov.</p

STAFFING MECHANISM TRIPLE HELIX

The article discusses the problems of organization of scientific and production activities with the aim of import substitution as a systemic problem of the national economy. The authors believe that the most appropriate theoretical basis is the mechanism of the triple helix, with some adaptation to modern conditions. This tool can make only with qualified personnel, who must be prepared according to the “dual education”. Recommendations for the integrated management of human capital development

STAFFING MECHANISM TRIPLE HELIX

The article discusses the problems of organization of scientific and production activities with the aim of import substitution as a systemic problem of the national economy. The authors believe that the most appropriate theoretical basis is the mechanism of the triple helix, with some adaptation to modern conditions. This tool can make only with qualified personnel, who must be prepared according to the “dual education”. Recommendations for the integrated management of human capital development

Morphology and Genetics of the Ciscoes (Actinopterygii: Salmoniformes: Salmonidae: Coregoninae: Coregonus) from the Solovetsky Archipelago (White Sea) as a Key to Determination of the Taxonomic Position of Ciscoes in Northeastern Europe

Background: The characteristic feature of the genus <i>Coregonus</i> is the multitude of nominal species of obscure identity. The northeastern Europe is inhabited by, inter alia—the vendace, <i>Coregonus albula</i> (Linnaeus, 1758)—considered the European cisco—and the least cisco, <i>C. sardinella</i> Valenciennes, 1848—often referred to as the Siberian species. There is a large area in where the ranges of both species overlap. Using morphological- as well as genetic tools we attempted to test the working hypothesis that the <i>Coregonus</i> fish (ciscoes) inhabiting the above-mentioned transitional zone represent a single species. Materials and methods: Within 1995–2009 we collected 344 ciscoes from five lakes in Bolshoy Solovetsky Island and determined diagnostic morphological traits for the two species. For some samples, the polymorphism of the creatine kinase isoloci (<i>CK-A1,2</i>*) and the fragment of mitochondrial DNA (mtDNA) encoding the subunit 1 of NADH-dehydrogenize complex (<i>ND-1</i> fragment) was also studied. Results: According to one of the main taxonomical characteristics—the number of vertebrae—the cisco of Solovetsky Island occupies an intermediate position between <i>C. albula</i> and <i>C. sardinella</i>. The molecular markers,however, did not reveal any differences between the ciscoes of Bolshoy Solovetsky Island and the vendace found elsewhere. All specimens had the type allele of creatine kinase <i>(CK-A*100)</i> which was considered to be typical for C. albula at other locations as well as the haplotype E of mtDNA widespread in vendace populations. Conclusion: The cisco from Solovetsky Island is more similar to typical vendace. Differences in some morphological traits between Solovetsky Island populations and the vendace from elsewhere are likely to reflect adaptation to environmental conditions. Thus it appears that morphological criteria do not allow reliable differentiation between two forms of ciscoes as well as between least cisco and vendace because they are influenced by environmental conditions. We believe that the presence of populations with intermediate features is a strong argument for combining <i>C. albula</i> and <i>C. sardinella</i> into a single species (<i>C. albula</i>)

Characteristic individual-psychological characteristics of students with limited functionality

The author describes the individual-psychological characteristics of students with limited functionality depending on the nosological form of the diseaseИзучены индивидуально-психологические особенности студентов с ограниченными функциональными возможностями в зависимости от нозологической формы заболевани

Individual-psychological characteristics of students with limited functionality

The author describes the individual-psychological characteristics of students with limited functionality depending on the nosological form of the diseaseИзучены индивидуально-психологические особенности студентов с ограниченными функциональными возможностями в зависимости от нозологической формы заболевани

Electrocatalytic oxidation and flow-injection determination of sulfur amino acids on a glassy carbon electrode modified by a nickel(II) polytetrasulfophthalocyanine film

The electrochemical oxidation of sulfur amino acids, i.e., cysteine, cystine, and methionine, is studied on a glassy carbon electrode modified by a film of nickel(II) polytetrasulfophthalocyanine (poly-NiTsPc). Poly-NiTsPc demonstrates a selective mediator activity in the oxidation of sulfur amino acids, depending on the pH of solution. The proper conditions for fabricating a polymer film on the surface of glassy carbon are found and the conditions of registering the maximal electrocatalytic effect on the modified electrode are determined. A procedure is proposed for the voltammetric determination and amperometric detection of cysteine, cystine, and methionine on an electrode coated by a poly-NiTsPc film under the conditions of flow-injection analysis (FIA). The linear relation of the electrocatalytic response of a composite electrode to amino acid concentration is observed to the level n × 10 -6 M in the static mode and n × 10-9 M under FIA conditions. © 2013 Pleiades Publishing, Ltd

The basic characteristics of development of agriculture in the kurgan region in the 2009-2013 period

Agriculture plays a significant the role in the economy of the Urals federal district, which in terms of gross agricultural production ranks fourth in Russia. Kurgan region is making a significant contribution to agricultural production of the district.Сельское хозяйство играет значительную роль в экономике Уральского федерального округа, который по объему валового производства сельскохозяйственной продукции занимает четвертое место в России. Курганская область вносит существенный вклад в производство продукции сельского хозяйства округа