Recognition of interferon-inducible sites, promoters, and enhancers

BACKGROUND: Computational analysis of gene regulatory regions is important for prediction of functions of many uncharacterized genes. With this in mind, search of the target genes for interferon (IFN) induction appears of interest. IFNs are multi-functional cytokines. Their effects are immunomodulatory, antiviral, antibacterial, and antitumor. The interaction of the IFNs with their cell surface receptors produces an activation of several transcription factors. Four regulatory factors, ISGF3, STAT1, IRF1, and NF-κB, are essential for the function of the IFN system. The aim of this work is the development of computational approaches for the recognition of DNA binding sites for these factors and computer programs for the prediction of the IFN-inducible regions. RESULTS: We developed computational approaches to the recognition of the binding sites for ISGF3, STAT1, IRF1, and NF-κB. Analysis of the distribution of these binding sites demonstrated that the regions -500 upstream of the transcription start site in IFN-inducible genes are enriched in putative binding sites for these transcription factors. Based on selected combinations of the sites whose frequencies were significantly higher than in the other functional gene groups, we developed methods for the prediction of the IFN-inducible promoters and enhancers. We analyzed 1004 sequences of the IFN-inducible genes compiled using microarray data analyses and also about 10,000 human gene sequences from the EPD and RefSeq databases; 74 of 1,664 human genes annotated in EPD were significantly IFN-inducible. CONCLUSION: Analyses of several control datasets demonstrated that the developed methods have a high accuracy of prediction of the IFN-inducible genes. Application of these methods to several datasets suggested that the number of the IFN-inducible genes is approximately 1500–2000 in the human genome

Infectious lesions of placenta as cause of miscarriage

Analysis of the literature demonstratesimportant role played of infections in causes of miscarriage. The paper is based upon retrospective analysis of 12371 screening results of histological and selective immunohistochemical studies of placentas in 2009-12. Preterm births were in 706 cases (5.71%). Infection of the placenta was noted in early preterm labor in all cases (100%), and in premature labor at 28-36 weeks of gestation – in 97.35% of natural delivery cases and in 92.09% when cesarean delivery. Are described the typical structural changes that allow to suspect infections caused by Treponema pallidum, herpes viruses, human immunodeficiency virus, parvovirus with following verification by immunohistochemical study

Analysis of whole-genome binding patterns of GAGA and CNC transcription factors during Drosophila melanogaster development

On the basis of available data of ChIP-seq and ChIPchip experiments performed using antibodies against GAGA and CNC transcription factors, genome-wide binding mapping of these factors at hours 0–12 and 16–24 of Drosophila embryogenesis, as well as on white pre-pupae stage, was conducted. It was shown that the bulk of GAGA and CNC binding falls into promoter regions and introns, with the maximal density of peaks in the vicinity of the transcription start site. Moreover, in both 0–12 and 16–24 hour old embryos GAGA and CNC are frequently co-localized, while on white pre-pupae stage there is no co-localization of these factors on a genome–wide scale. In order to select a set of genes potentially co-regulated by GAGA and CNC, the study of their co-binding in annotated regulatory regions (promoter areas and segments corresponding to the 5’-UTR and 3’-UTR of mRNA) was performed. The results obtained clearly demonstrated that the sets of genes characterized by co-binding of both factors vary greatly at different stages. Thus from 353 genes with overlapped GAGA and CNC binding loci on the 0–12 hour old embryos and 611 genes on the 0–12 hour old embryos only 61 genes “belong” to both stages. For an explanation it is proposed that different sets of target genes are regulated by combinations of various GAGA and CNC isoforms, which are characterized by distinct expression patterns during drosophila embryogenesis. Functional annotation analysis of genes, in whose regulatory regions both GAGA and CNC were found at all investigated stages, demonstrates enrichment by genes controlling embryogenesis, neurogenesis and wing development. The data obtained suggest the interaction of GAGA and CNC during D. melanogaster embryogenesis

Application of alternative <i>de novo</i> motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites

The most popular model for the search of ChIP-seq data for transcription factor binding sites (TFBS) is the positional weight matrix (PWM). However, this model does not take into account dependencies between nucleotide occurrences in different site positions. Currently, two recently proposed models, BaMM and InMoDe, can do as much. However, application of these models was usually limited only to comparing their recognition accuracies with that of PWMs, while none of the analyses of the co-prediction and relative positioning of hits of different models in peaks has yet been performed. To close this gap, we propose the pipeline called MultiDeNA. This pipeline includes stages of model training, assessing their recognition accuracy, scanning ChIP-seq peaks and their classif ication based on scan results. We applied our pipeline to 22 ChIP-seq datasets of TF FOXA2 and considered PWM, dinucleotide PWM (diPWM), BaMM and InMoDe models. The combination of these four models allowed a signif icant increase in the fraction of recognized peaks compared to that for the sole PWM model: the increase was 26.3 %. The BaMM model provided the main contribution to the recognition of sites. Although the major fraction of predicted peaks contained TFBS of different models with coincided positions, the medians of the fraction of peaks containing the predictions of sole models were 1.08, 0.49, 4.15 and 1.73 % for PWM, diPWM, BaMM and InMoDe, respectively. Thus, FOXA2 BSs were not fully described by only a sole model, which indicates theirs heterogeneity. We assume that the BaMM model is the most successful in describing the structure of the FOXA2 BS in ChIP-seq datasets under study

Prevention of Cardioembolic Complications in Patients with Atrial Fibrillation: Efficacy and Safety of Left Atrial Appendage Isolation and Oral Anticoagulants

Aim. To study the outcomes frequency and structure in patients with atrial fibrillation (AF) depending on the cardioembolic events preventing method: left atrial appendage (LAA) isolation, direct oral anticoagulants (DOACs) or warfarin.Material and methods. A prospective observational study included patients with AF and high risk of cardioembolic complications and without contraindications to anticoagulants. Patients who refused long-term oral anticoagulants taking underwent LAA isolation, the rest of the patients received DOACs or warfarin. The observation period was 3 years. Mortality, cardioembolic complications and major bleeding (according to GARFIELD criteria) cumulative incidence was assessed.Results. We included 245 patients: 46 patients were treated with LAA isolation, 100 with warfarin, and 99 with DOACs. Multivariate regression analysis demonstrated a statistically significant advantage of LAA occluder in terms of combined endpoint achieving frequency compared to warfarin (hazard ratio [HR] 3.10; 95% confidence interval [CI] 1.01-9.54; p=0.049), and to DOACs (HR 3.44, 95% CI 1.15-10.29; p=0.027). A similar result was obtained for all-cause mortality (HR 5.24; 95% CI 1.12-24.55; p=0.036 and HR 5.58; 95% CI 1.22-25.49; p=0.027, respectively). There were no significant differences in bleeding rates between the groups.Conclusion. This observational study demonstrates the superiority of LAA isolation as a first-line therapy over DOACs and warfarin in patients with AF and high risk of cardioembolic complications. Randomized trials are required to confirm these observations

Efficacy and safety of left atrial appendage closure in patients with atrial fibrillation and high thromboembolic and bleeding risk

Aim. To compare the incidence of thromboembolic and hemorrhagic events after left atrial appendage occlusion (LAAO) or without prevention of thromboembolic events (TEEs) during prospective follow-up of patients with atrial fibrillation (AF) and a high risk of ischemic stroke (IS) who have contraindications to long-term anticoagulant therapy.Material and methods. The study included 134 patients with AF, a high risk of IS, and contraindications to long-term anticoagulation. Patients were divided into 2 groups as follows: the first group included patients who underwent LAAO (n=74), while the second one — those who did not undergo any TEE prevention (n=60). The follow-up period was 3 years. The cumulative rate of all-cause mortality, IS, transient ischemic attacks (TIA), and systemic embolism (SE) was taken as the primary efficacy endpoint. The primary safety endpoint included major bleeding according to GARFIELD registry criteria.Results.  The rate of composite efficacy endpoint in the LAAO group was significantly lower than in the group without thromboembolic prophylaxis (5,2 vs 17,4 per 100 patient-years; adjusted odds ratio (OR), 4,08; 95% confidence interval (CI): 1,7-9,5; p=0,001). The rate of major bleeding was comparable in both groups (2,4 in the LAAO group vs 1,3 per 100 patient-years in the group without thromboembolic prophylaxis; adjusted OR, 0,55; 95% CI: 0,1-3,09; p=0,509). In addition, the event rate of net clinical benefit (all-cause mortality + ischemic stroke/TIA/SE + major bleeding) in the LAAO group was also significantly lower (5,9 vs 18,2 per 100 patient-years; adjusted OR, 3,0; 95% CI: 1,47-6,36; p=0,003).Conclusion. Among patients with AF and contraindications to long-term anticoagulation after 3 years of follow-up, LAAO demonstrated the significant reduction of cumulative rate of all-cause mortality and non-fatal thromboembolic events. At the same time, the frequency of major bleeding was comparable between the groups, even taking into account access-site bleeding and postoperative antithrombotic therapy (ATT)-associated bleeding in the LAAO group. Further randomized clinical trials are required to confirm these data

The combination of traditional cardiorespiratory markers during treadmill testing “to failure” in athletes, depending on professional activity

Exercise tolerance test with the use of the spiroergometry technique is a reliable diagnostic method which provides objective information about cardiorespiratory system condition when performing physical activity. Both new and traditional, well-proven cardiorespiratory markers obtained in the process of treadmill testing “to failure”, are described in this article. The nature of the influence of physical exertion on the indicators of cardiorespiratory system functional activity is presented. The interpretation for planning and subsequent monitoring of the training process in athletes of various professional activities is proposed

Инфекционные поражения последа как причина невынашивания беременности

Analysis of the literature demonstratesimportant role played of infections in causes of miscarriage. The paper is based upon retrospective analysis of 12371 screening results of histological and selective immunohistochemical studies of placentas in 2009-12. Preterm births were in 706 cases (5.71%). Infection of the placenta was noted in early preterm labor in all cases (100%), and in premature labor at 28-36 weeks of gestation – in 97.35% of natural delivery cases and in 92.09% when cesarean delivery. Are described the typical structural changes that allow to suspect infections caused by Treponema pallidum, herpes viruses, human immunodeficiency virus, parvovirus with following verification by immunohistochemical study. Анализ литературных данных свидетельствует, что среди причин невынашивания беременности важную роль играет инфекционный фактор. В статье на основании ретроспективного анализа 12 371 результата скринингового гистологического и выборочного иммуногистохимического исследования последов за 2009–2012 гг. показано, что преждевременные роды были в 706 случаях (5,71%). Инфицирование последа отмечалось при ранних преждевременных родах во всех случаях (100%), а при преждевременных родах на сроке беременности 28–36 недель – в 97,35% при естественном родоразрешении и 92,09% – при родоразрешении путем кесарева сечения. Дана характеристика структурных изменений, которые позволяют заподозрить наличие инфекций, вызванных Treponema pallidum, герпес-вирусами, вирусом иммунодефицита человека, парвовирусом с последующей верификацией при иммуногистохимическом исследовании.

Study of the structure and kinematics of the NGC 7465/64/63 triplet galaxies

This paper is devoted to the analysis of new observational data for the group of galaxies NGC 7465/64/63, which were obtained at the 6-m telescope of the Special Astrophysical Observatory of the Russian Academy of Sciences (SAO RAS) with the multimode instrument SCORPIO and the Multi Pupil Fiber Spectrograph. For one of group members (NGC 7465) the presence of a polar ring was suspected. Large-scale brightness distributions, velocity and velocity dispersion fields of the ionized gas for all three galaxies as well as line-of-sight velocity curves on the basis of emission and absorption lines and a stellar velocity field in the central region for NGC 7465 were constructed. As a result of the analysis of the obtained information, we revealed an inner stellar disk (r ~ 0.5 kpc) and a warped gaseous disk in addition to the main stellar disk, in NGC 7465. On the basis of the joint study of photometric and spectral data it was ascertained that NGC 7464 is the irregular galaxy of the IrrI type, whose structural and kinematic peculiarities resulted most likely from the gravitational interaction with NGC 7465. The velocity field of the ionized gas of NGC 7463 turned out typical for spiral galaxies with a bar, and the bending of outer parts of its disk could arise owing to the close encounter with one of galaxies of the environment.Comment: 20 pages, 6 figure