[G4-quadruplexes and genome instability].

A comparative analysis in silico of distribution of nucleotide sequences that predispose to formation of non-canonical DNA structure of G-quadruplexes, closely related with gene expression regulation and double strand DNA breaks, within vertebrata and yeast nuclear and mitochondrial genomes was carried out. Data on preferable localization of potential quadruplexes within non-coding sequences, their evolutionary conservation, and existing homology between them in mitochondrial and nuclear genomes were obtained. A possible interrelation between quadruplexes, Pif1 helicase and genomic instability is discussed.

Gene set analysis for self-contained tests: complex null and specific alternative hypotheses.

MOTIVATION: The analysis of differentially expressed gene sets became a routine in the analyses of gene expression data. There is a multitude of tests available, ranging from aggregation tests that summarize gene-level statistics for a gene set to true multivariate tests, accounting for intergene correlations. Most of them detect complex departures from the null hypothesis but when the null hypothesis is rejected, the specific alternative leading to the rejection is not easily identifiable. RESULTS: In this article we compare the power and Type I error rates of minimum-spanning tree (MST)-based non-parametric multivariate tests with several multivariate and aggregation tests, which are frequently used for pathway analyses. In our simulation study, we demonstrate that MST-based tests have power that is for many settings comparable with the power of conventional approaches, but outperform them in specific regions of the parameter space corresponding to biologically relevant configurations. Further, we find for simulated and for gene expression data that MST-based tests discriminate well against shift and scale alternatives. As a general result, we suggest a two-step practical analysis strategy that may increase the interpretability of experimental data: first, apply the most powerful multivariate test to find the subset of pathways for which the null hypothesis is rejected and second, apply MST-based tests to these pathways to select those that support specific alternative hypotheses. CONTACT: gvglazko@uams.edu or yrahmatallah@uams.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

[siRNAs with high specificity to the target: a systematic design by CRM algorithm].

'Off-target' silencing effect hinders the development of siRNA-based therapeutic and research applications. Common solution to this problem is an employment of the BLAST that may miss significant alignments or an exhaustive Smith-Waterman algorithm that is very time-consuming. We have developed a Comprehensive Redundancy Minimizer (CRM) approach for mapping all unique sequences ("targets") 9-to-15 nt in size within large sets of sequences (e.g. transcriptomes). CRM outputs a list of potential siRNA candidates for every transcript of the particular species. These candidates could be further analyzed by traditional "set-of-rules" types of siRNA designing tools. For human, 91% of transcripts are covered by candidate siRNAs with kernel targets of N = 15. We tested our approach on the collection of previously described experimentally assessed siRNAs and found that the correlation between efficacy and presence in CRM-approved set is significant (r = 0.215, p-value = 0.0001). An interactive database that contains a precompiled set of all human siRNA candidates with minimized redundancy is available at http://129.174.194.243. Application of the CRM-based filtering minimizes potential "off-target" silencing effects and could improve routine siRNA applications.

The effect of mutations altering biogenic amine metabolism in Drosophila on viability and the response to environmental stresses.

Dopamine (DA) content, tyrosine decarboxylase (TDC) activity and survival were studied under normal and environmental stress conditions in the ste and e strains carrying ebony mutation increasing DA level and the octopamineless strain Tbetah(nM18) of Drosophila melanogaster. Wild-type strains Canton S and Oregon R, and strain p845 from which Tbetah(nM18) strain was derived were used as controls. Sexual dimorphism of TDC activity, DA content, and survival in flies of all D. melanogaster strains under study was found. Tbetah(nM18) mutation sharply reduced TDC activity in females, while ebony had no such effect. DA content and survival under heat stress in Tbetah(nM18) flies did not differ from those in the wild type. ste and e flies had drastically increased DA content under normal conditions, dramatically decreased survival under heat stress, but increased survival under starvation. DA content and survival under heat stress were also studied in the reciprocal hybrids (males) F(1) of the cross D. virilis strains 101 (wild type) and 147 with X-linked mutation, which significantly increases DA content. 147x101 males had a considerably higher DA content and lower survival than 101x147 ones. Individuals of all D. melanogaster strains under study developed the stress reaction, as judged by changes in TDC activity and DA levels. The role of biogenic amines in the stress reaction development and adaptation to environmental stresses in Drosophila is discussed. Arch. Insect Biochem. Physiol. 55:55-67, 2004.

The Wilhelmine E. Key 2001 Invitational Lecture. Estimation of divergence times for a few mammalian and several primate species.

Statistical methods for estimating divergence times by using multiprotein gamma distances are discussed. When a large number of proteins are used, even a small degree of deviation from the molecular clock hypothesis can be detected. In this case, one may use the stem-lineage method for estimating divergence times. However, the estimates obtained by this method are often similar to those obtained by the linearized tree method. Application of these methods to a dataset of 104 proteins from several vertebrate species indicated that the divergence times between humans and mice and between mice and rats are about 96 and 33 million years (MY) ago, respectively. These estimates were obtained by assuming that birds and mammals diverged 310 MY ago. Similarly application of the methods to the protein sequence data from primate species indicated that the human lineage separated from the chimpanzee, gorilla, Old World monkeys, and New World monkeys about 6.0, 7.0, 23.0, and 33.0 MY ago, respectively. In this case the use of two calibration points, that is, the divergence time (13 MY ago) between humans and orangutans and between primates and artiodactyls (90 MY ago) gave essentially the same estimates.

[Context organization of mRNA 5'-untranslated regions of higher plants]. / Kontekstnaia organizatsiia 5'-netransliruemykh raionov mRNK genov vysshikh rastenii.

Computer analysis of nucleotide sequences of 5'-untranslated regions (5'-UTR) of higher plants mRNA adopted from the EMBL nucleotide sequence databank was carried out. It was demonstrated that the average nucleotide frequencies of the leader sequences and adjacent regions of basal promoters are similar, whereas introns and 3'-UTR have a higher content of T and a lower content of C. A particular 5'-UTR contextual feature is a misbalance in the content of complementary nucleotides; probably a stable secondary structure adversely affects the translation properties of the leader sequence. About 20% of 5'-UTR contain AUG triplets, which is twice the earlier estimate. Considered are the properties of leader open reading frames (uORF), the possible causes of their high content in 5'-UTRs of eukaryotic mTNAs, and correlations between the features of uORFs and of the protein-encoding sequence of the gene. It is demonstrated that in effectively translated mRNAs the leader AUG triplets are more frequently located in a nonoptimal context, whereas terminating codons of uORFs more frequently exist in the optimal one. A hypothesis is put forward that the efficiency of termination at the uORF stop codon might substantially interfere with the mRNA translation activity.

[Interaction of hormones in controlling reproductive function of Drosophila females under stressful conditions is genetically determined]. / Vzaimodeistvie gormonov v kontrole reproduktivnoi funktsii samok Drosophila v usloviiakh stressa geneticheski determinirovano.

The effect of heat stress (38 degrees C) on the content of octopamine (OA) and 20-hydroxyecdysone (20HE) was studied under normal and stressful conditions in adult flies of Drosophila virilis lines contrasting in the level of the juvenile hormone (JH). The wild-type flies (line 101) exhibited a pronounced sex dimorphism for the content of both OA and 20HE, which was substantially lower in this line than in flies of the mutant line 147. The level of both hormones increased in flies of line 101 exposed to heat stress, whereas it remained unchanged in flies of line 147 under the same conditions. The effect of heat stress on the level of JH metabolism and fertility was also studied in D. melanogaster wild-type lines and lines carrying mutations in genes responsible for OA and DA syntheses. In octopamineless females of the T beta hnM18 line and in females of the Ste line characterized by a doubled content of DA, JH degradation differed from normal: it was increased in both young and mature T beta hnM18 females, while decreased in young and increased in mature Ste flies. Fertility was substantially lower in the Ste than in the wild-type line. Flies of all of the D. melanogaster lines produced a stress response; however, in mutant lines, both fertility and stress reactivity of the systems controlling JH metabolism differed significantly from that of the wild-type lines. The role of JH, 20HE, OA, and DA interaction in regulation of Drosophila reproduction under stressful conditions is discussed.

Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix.

Scaffold/matrix-associated region (S/MAR) sequences are DNA regions that are attached to the nuclear matrix, and participate in many cellular processes. The nuclear matrix is a complex structure consisting of various elements. In this paper we compared frequencies of simple nucleotide motifs in S/MAR sequences and in sequences extracted directly from various nuclear matrix elements, such as nuclear lamina, cores of rosette-like structures, synaptonemal complex. Multivariate linear discriminant analysis revealed significant differences between these sequences. Based on this result we have developed a program, ChrClass (Win/NT version, ftp.bionet.nsc.ru/pub/biology/chrclass/chrclass.zip), for the prediction of the regions associated with various elements of the nuclear matrix in a query sequence. Subsequently, several test samples were analyzed by using two S/MAR prediction programs (a ChrClass and MAR-Finder) and a simple MRS criterion (S/MAR recognition signature) indicating the presence of S/MARs. Some overlap between the predictions of all MAR prediction tools has been found. Simultaneous use of the ChrClass, MRS criterion and MAR-Finder programs may help to obtain a more clearcut picture of S/MAR distribution in a query sequence. In general, our results suggest that the proportion of missed S/MARs is lower for ChrClass, whereas the proportion of wrong S/MARs is lower for MAR-Finder and MRS.

Use of mutation spectra analysis software.

The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called "hotspots," in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG-PUBL program, (FTP: sunsite.unc.edu/pub/academic/biology/dna-mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis.

Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms.

When many protein sequences are available for estimating the time of divergence between two species, it is customary to estimate the time for each protein separately and then use the average for all proteins as the final estimate. However, it can be shown that this estimate generally has an upward bias, and that an unbiased estimate is obtained by using distances based on concatenated sequences. We have shown that two concatenation-based distances, i.e., average gamma distance weighted with sequence length (d(2)) and multiprotein gamma distance (d(3)), generally give more satisfactory results than other concatenation-based distances. Using these two distance measures for 104 protein sequences, we estimated the time of divergence between mice and rats to be approximately 33 million years ago. Similarly, the time of divergence between humans and rodents was estimated to be approximately 96 million years ago. We also investigated the dependency of time estimates on statistical methods and various assumptions made by using sequence data from eubacteria, protists, plants, fungi, and animals. Our best estimates of the times of divergence between eubacteria and eukaryotes, between protists and other eukaryotes, and between plants, fungi, and animals were 3, 1.7, and 1.3 billion years ago, respectively. However, estimates of ancient divergence times are subject to a substantial amount of error caused by uncertainty of the molecular clock, horizontal gene transfer, errors in sequence alignments, etc.

Computer prediction of sites associated with various elements of the nuclear matrix.

Attachment regions of the eukaryotic chromosomal DNA to the nuclear scaffold/matrix (S/MARs) participate in various important cellular processes. However, no obvious characteristics common for these nucleotide sequences have been revealed, except that S/MARs are non-coding sites containing putative regulatory elements and binding sites of DNA-topoisomerase II. Heterogeneity among S/MARs can be caused by a variety of biological factors. In this paper, the accuracy of two S/MARs prediction programs, MAR-Finder (Singh, Kramer and Krawetz, 1997) and ChrClass (Glazkov, Rogozin and Glazko, 1998) are compared and it is concluded that both programs can be recommended for analysis of eukaryotic genomes. However, results of their prediction should be interpreted with caution since estimation of prediction accuracy of both programs needs further analysis. Problems of S/MARs prediction are illustrated on several examples of human protein-coding genes, repeated elements and the beta-globin locus from different mammalian species. Results of our analysis suggest that the proportion of missed S/MARs is lower for ChrClass, whereas the proportion of wrong S/MARs is lower for MAR-Finder (a default set of parameters).

[The mutational spectra of gene p53 in different types of tumors]. / Issledovanie mutatsionnykh spektrov gena p53 v razlichnykh tipakh opukholei.

The comparative analysis of the frequencies of nucleotide exchanges in mutational spectra of gene p53 (5-8 exons) between germline cancer-prone families (Li-Fraumeni syndrome), between somatic mutations in the tumors of different histogenesis and cell lines, obtained from them, was carried out. The nucleotide positions with high level of mutation events (mutational "hot spots"), typical for germline mutational spectra, tissue-specific patterns of their disappearing and appearing of new ones in solid tumors in vivo, nearly complete absence of "hot spots" in lymphomas and cell lines in vitro were revealed. The obtained results allowed to suggest, that one of the leading factor controlling hot-spots distribution in 5-8 exons of gene p53 is the specificity of cell division conditions in vivo and in vitro.

[The interrelations between karyotypic stability and interchromosomal associations in mammalian cells]. / Izuchenie vzaimosviazei mezhdu kariotipicheskoi stabil'nosti i mezhkhromosomnymi assotsiatsiiami v kletkakh mlekopitaiushchikh.

The interchromosome associations between heterologous chromosomes (for the type of Robertsonian translocations); frequencies of the association between individual chromosomes (identified by G-bands) and mouse line pecularities, the directions of cytodifferentiation, the stages of cell neoplastic transformation in cell populations of various origin have been estimated. The presence of interrelations between individual chromosome associations and genetic and cytological cell characteristics with the use of different mathematical methods of analysis has been revealed.

The subclass approach for mutational spectrum analysis: application of the SEM algorithm.

Analysis and comparison of mutational spectra represents an important problem in molecular biology. To analyse a mutational spectra we apply an algorithm based on the SEM subclass approach (Simulation, Expectation, Maximization). The algorithm tries to classify the mutational sites according to different mutation probabilities, and each site should belong to one class. Each class is approximated by binomial distribution and thus any real mutational spectrum is regarded as a mixture of binomial distributions. The separation process runs iteratively. Each iteration includes the simulation, maximization and estimation procedures. To evaluate the quality of the classification results, the X2 test is used. The algorithm has been checked on random spectra with preset parameters and on real mutational spectra. As has been shown, 17 out of 19 analysed real mutational spectra can be divided into two or more classes of sites, of which one contains hotspots of mutation. For the G:C-->A:T mutational spectra induced by Sn1 alkylating mutagenes (11 spectra) the classification accuracy was 0.95. To test different site volumes, each Sn1-induced spectrum was divided into the G-->A and C-->T spectra. The classification accuracy for these spectra was 0.96. From the analysis of classification errors it is possible to suggest that at least part of them cannot be ascribed to the faults of the algorithm but are caused by some special features of the mutagenesis itself. The results of the real data are in good relation with existing knowledge. The approach we present is an attempt to formalize the concept of a "mutational hotspot". The program implementing the SEM algorithm is available on the Web server (http:/(/)www.itba.mi.cnr.it/webmutation).

[The characteristics of the chromosomal level of variability in mice]. / Nekotorye kharakteristiki khromosomnogo urovnia izmenchivosti u myshei.

The analysis of the order of chromosome involving to interchromosome associations by the type of Robertsonian translocation (RB) in 28 cell populations in relation with three factors: their origin from different mouse lines (CBA/Ca, C3H/He, C57BL/6, BALB/c), direction of cytodifferentiation (fibroblasts and leucocytes) and the stage of its disruption (minimal, maximal and medial tumorigenicity) was carried out. The influence of all three factors on the frequencies of individual chromosome involving in RB was revealed.

[Interlocus associations and their variability in cattle]. / Mezhlokusnye assotsiatsii i ikh izmenchivost' u krupnogo rogatogo skota.

The results of analysis of interloci associations between two pairs of syntenic loci (transferrin and ceruloplasmin, receptor for vitamin D and kappa-casein) and two non-syntenic ones (amylase-1 and post-transferrin 2) in two cattle groups of Red Steppe breed (infected and uninfected by bovine leukosis virus) and in two groups of Black-and-White Holsteins (from relatively "pure" zone and from the 10 km zone of Chernobyl NPP) were presented. It is found that "linkage disequilibrium" between loci is observed independent of their synteny. The data obtained allowed the authors to suppose, that the interloci associations are rather controlled by different factors of artificial and natural selection than by the genetic linkages between genes.

[Experimental and calculated spectra of the amplicons UBC-85 and UBC-126 (RAPD-PCR)]. / Eksperimental'nye i raschetnye spektry amplikonov UBC-85 i UBC-126 (RAPD-PCR).

The comparative analysis of experimental amplification spectrum in 13 Ungulata species and counting ones in DNA sequences of different taxa in GenBank (mammalian, other vertebrate, invertebrate, viruses, prokaryote) with the uses of RAPD-PCR primers UBC-85 and UBC-126 was carried out. The particularities of the distribution of amplicons' frequencies in experimental and counting spectrums were revealed, for some of them the similar increased frequencies in mammalian and prokaryotic species were observed.

[The heterogeneity of the cytogenetic variability in the bone marrow cells of laboratory and wild rodents in the exclusion zone of the Chernobyl Atomic Electric Power Station]. / Geterogennost' tsitogeneticheskoi izmenchivosti v kletkakh kostnogo mozga laboratornykh i dikikh gryzunov v usloviiakh zony otchuzhdeniia Chernobyl'skoi AES.

Analysis of the characters of cytogenetic variabilities and correlative interrelations between them revealed the group specificities of karyotype instability in bone marrow cells of some lines of laboratory and of wild mice under the conditions of increased radionuclide pollution in the Chernobyl zone. The complex correlative interrelations between the frequencies of cytogenetic anomalies and the character of cell division (the number of metaphases, binucleated leukocytes per 1000 cells) were observed. The obtained data indicate the stimulatory influence of chronic low doses of ionizing radiation on the manifestation of spontaneous mutagenesis, which has own genotype specific characteristics.