Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data

The expression level of each gene is controlled by its regulatory regions, which determine the precise regulation in a tissue-specific manner, according to the developmental stage of the body and the necessity of a response to external stimuli. Nucleotide substitutions in regulatory gene regions may modify the affinity of transcription factors to their specific DNA binding sites, affecting the transcription rates of genes. In our previous research, we found that genes controlling the sensory perception of smell and genes involved in antigen processing and presentation were overrepresented significantly among genes with high SNP contents in their promoter regions. The goal of our study was to reveal functional features of human genes containing extremely small numbers of SNPs in promoter regions. Two functional groups were found to be overrepresented among genes whose promoters did not contain SNPs: (1) genes involved in gene-specific transcription and (2) genes controlling chromatin organization. We revealed that the 5′-regulatory regions of genes encoding transcription factors and chromatin-modifying proteins were characterized by reduced genetic variability. One important exception from this rule refers to genes encoding transcription factors with zinc-coordinating DNA-binding domains (DBDs), which underwent extensive expansion in vertebrates, particularly, in primate evolution. Hence, we obtained new evidence for evolutionary forces shaping variability in 5′-regulatory regions of genes

NPRD: Nucleosome Positioning Region Database

Nucleosome Positioning Region Database (NPRD), which is compiling the available experimental data on locations and characteristics of nucleosome formation sites (NFSs), is the first curated NFS-oriented database. The object of the database is a single NFS described in an individual entry. When annotating results of NFS experimental mapping, we pay special attention to several important functional characteristics, such as the relationship between type of gene activity and nucleosome positioning, the influence of non-histone proteins on nucleosome formation, type of the variant of nucleosome positioning (translational or rotational), indication of tissue types and states of cell activity, description of experimental methods used and accuracy of nucleosome position determination, and the results of applying theoretical and computer methods to the analysis of contextual and conformational DNA properties. At present, the NPRD database contains 438 entries and integrates the data described in 124 original papers. The database URL: http://srs6.bionet.nsc.ru/srs6/. Then click the button ‘Databank’ and open the link NUCLEOSOME

Protecting the Kidney in Liver Transplant Recipients: Practice‐Based Recommendations From the American Society of Transplantation Liver and Intestine Community of Practice

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134132/1/ajt13765_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134132/2/ajt13765.pd

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

Dynamics of spin correlations in the spin-1/2 isotropic XY chain in a transverse field

Dynamic xx spin pair correlation functions for the isotropic spin-1/2 XY chain are calculated numerically for long open chains in the presence of a transverse magnetic field at finite temperature. As an application we discuss the temperature dependence of the spin-spin relaxation time in PrCl_3.Comment: 2 pages, latex, 2 figures, abstract of the paper presented at Ampere Summer School ``Applications of Magnetic Resonance in Novel Materials'' Nafplion, Greece, 3-9 September, 2000, partially published in J. Phys. A: Math. Gen. 33, 3063 (2000

The therapeutic effect of antidisbiotic means on the mucous sheath of rats digestive tract, obtaining peroxidized sunflower oil

Aim: Determine the therapeutic effect of antidysbiosis agents (ADA) on the condition of the mucous membrane of the digestive tract when consumed per-oxidized sunflower oil (PSO). Materials and Methods: Rats were fed 4 g / kg of PSO for 75 days. From the 31st day, they were administered one of the following ADA with 300 mg / kg of food: kvertulin (quercetin + inulin + calcium citrate), lekvin (lecithin + kvertulin) and lysozyme-forte (lysozyme + quercetin + inulin + gelatin + calcium citrate). The activity of elastase, urease, lysozyme, catalase and the content of MDA were determined in the homogenates of the mucous cheeks, small and large intestine. The ratio of catalase activity and the content of MDA was calculated by the API index, and the ratio of the relative activities of urease and lysozyme - the degree of dysbiosis. Results: The consumption of PSO in rats in the mucous membranes of the digestive tract increases the activity of elastase, urease, MDA content and the degree of dysbiosis while reducing the activity of lysozyme, catalase and the API index. In rats treated with ADA, the activity of elastase, urease, MDA content, and the degree of dysbiosis decrease, but the activity of lysozyme and catalase increase. Conclusion: Peroxide intoxication causes the development of mucositis, which can be prevented by antidysbiosis agents

The influence of different pathogens on the lysozyme activity into tissues of rat oral cavity

Aim: To determine action of the different pathogens on the lysozyme activity into tissues of oral cavity and serum.Methods: The lysozyme activities was determined into oral mucosa cheek, tongue gum and serum of 158 white rats (11 series experiments). The pathogens were used: atropine, protamine sulfat, indometacyn, bee poison, hydrasine sulfat, cytostatic cyclofosfan, lincomycin, lipopolysaccharide, composition of antibiotic and omeprasol for ACBTResults: The  whole of pathogens decreased lysozyme activity (mean in 1,6-2,5 times) into oral tissues and on 16 % into serum. The specific lowering of lysozyme activities (Δ%/mg pathogen) was low most for lipopolysaccharide, especially after oral application usage (exceeding was in tens times).Conclusion: The lysozyme activity lowering may play significant role in pathogenesis of stomatologic diseases/ Lipopolysaccharide (LPS) send lysozyme activity lowering most especially after oral application. Probably, the antilysozyme action of pathogens realize by LPS. The stomatogenic factor in pathogenesis and profilactic of noninfection diseases is important

Associations of BCL-2 (RS17759659), CTLA-4 (RS231775), APO-1/FAS (RS2234767) genes polymorphisms with activity of proliferation and apoptosis in thyroid tissue of patients with nodular forms of goiter combined with autoimmune thyroiditis and thyroid adenoma

The study of apoptosis and proliferative activity in the thyroid gland (TG) tissue of patients with nodular goiter and autoimmune thyroiditis (NGAIT) and thyroid adenoma (TA) is based on the expression/density of Fas/FasL, BCL-2, p53, and Ki-67 markers assessment depending on the genetic polymorphisms of BCL-2 (rs17759659), CTLA-4 (rs231775) and APO-1/Fas (rs2234767) genes.Several mechanisms of thyroid cells' programmed killing are activated in NGAIT and TA with domination of Fas-induced apoptosis, which strongly associates with the BCL-2 gene's (rs17759659) promoter (F=25.33; p&lt;0.001) and almost six fold weaker associates with the CTLA-4 gene's (rs231775) promoter (F=4.23, p=0.017). Factors that decrease the likelihood of NGAIT and TA regardless of the CTLA-4 (rs231775) and APO-1/Fas (rs2234767) genes' genotypes are the high Ki-67 density and reduction of cells containing p53 or BCL-2 proteins (OR=0.07-0.17; 95% CI OR: 0.03-0.36; p&lt;0.001, and OR=0.08-0.11; 95% CI OR: 0.02-0.31; p&lt;0.001, re­spectively). High expression of surface Fas and FasL in lymphoid infiltration and de­struction of thyroid cells (stronger in GG-genotype carriers of the BCL-2 gene by 18.54% (pAA=0.043) and 36.18% (pAG=0.018), respectively) indicates the initiation of the external pathway of apoptosis through the caspase mechanism (effector caspase- 8)

Influence of oral fatty applications on biochemical indicators of inflammation and dysbiosis in the tissues of the rat mouth

Background. The negative impact on the body of high-fat nutrition largely depends on the fatty acid composition of edible fats and the presence of peroxidation products in them, which are formed during heat treatment. Despite the considerable number of studies on this issue, it remains unclear the nature of the influence of different dietary fats on the condition of the tissues of the oral cavity. The purpose of this study was to clarify this issue Methods. Ordinary (high-linoleic) sunflower oil, high-oleic sunflower oil and butter in the native state and after heat treatment were used. The experiments were carried out on 35 white rats with an average weight of 252±15 g, who were given oral applications of the above fats at a dose of 0.5 ml per rat for 3 days. After rat killing on the 4th day, the content of malondialdehyde (MDA), the activity of elastase, urease, lysozyme and catalase were determined in the cheek mucosa homogenate and in the gums. The degree of dysbiosis was calculated by the ratio of the relative activities of urease and lysozyme. The antioxidant-prooxidant API index was calculated from the ratio of catalase activity and MDA content Results. Oral applications of native and heat-treated oils cause a decrease in the MDA content in both tissues with the exception of heat-treated butter, applications of which do not reduce the MDA level. Applications of heat-treated oils increase the activity of elastase in the gums, and heat-treated sunflower oil in the cheek mucosa. Applications of native and heat-treated oils reduce the activity of catalase in the cheek and gums. The API index increases in the gums under the action of native oils and decreases under the action of thermally processed oils. Applications of butter (native and heat-treated) significantly reduce the activity of urease in the cheek mucosa. Sunflower and high-oleic sunflower oils tend to increase the activity of urease, the least pronounced for the latter. All oils except high-oleic sunflower, reduce the activity of lysozyme in both tissues and all oils increase the degree of dysbiosis (except butter in the cheek mucosa). The content of diene conjugates after heat treatment increased the most in butter, and the least in high-oleic sunflower oil. Conclusion. Oral applications of fats cause a decrease in the formation of active forms of oxygen in the tissues of the oral cavity, which causes the development of dysbiosis and inflammatory processes

Emergence of additional visible range photoluminescence due to aggregation of cyanine dye:astraphloxin on carbon nanotubes dispersed with anionic surfactant

Self-organization of organic molecules with carbon nanomaterials leads to formation of functionalized molecular nano-complexes with advanced features. We present a study of physical and chemical properties of carbon nanotube-surfactant-indocarbocyanine dye (astraphloxin) in water focusing on aggregation of the dye and resonant energy transfer from the dye to the nanotubes. Self-assembly of astraphloxin is evidenced in absorbance and photoluminescence depending dramatically on the concentrations of both the dye and surfactant in the mixtures. We observed an appearance of new photoluminescence peaks in visible range from the dye aggregates. The aggregates characterized with red shifted photoluminescence peaks at 595, 635 and 675 nm are formed mainly due to the presence of surfactant at the premicellar concentration. The energy transfer from the dye to the nanotubes amplifying near-infrared photoluminescence from the nanotubes is not affected by the aggregation of astraphloxin molecules providing important knowledge for further development of advanced molecular nano-complexes. The aggregation with the turned-on peaks and the energy transfer with amplified photoluminescence create powerful tools of visualization and/or detection of the nanotubes in visible and near-infrared spectral range, respectively, boosting its possible applications in sensors, energy generation/storage, and healthcare