Structural Characterization of the NodD Transcription Factor

Abstract Using computer analysis and modeling we studied NodD transcription factor which controls expression of nodulation genes of symbiotic nitrogen-fixing bacteria. On the basis of the amino acid sequences it was predicted that in the secondary structure of NodD protein it must be present ten alpha helices and three beta sheets which form two do mains after folding. Since NodD acts in oligo meric mode, it was analy zed all four known for other similar factors of transcription ways of assembly into dime rs. Using molecular docking the probable mechanism o f NodD act ivation by binding of low molecular weight inducer (on the model o f luteolin) was clarified

Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach

Nuclear DNA of metazoans is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). DNA is anchored to the NM by non-coding sequences known as matrix attachment regions (MARs). There are no consensus sequences for identification of MARs and not all potential MARs are actually bound to the NM constituting loop attachment regions (LARs). Fundamental processes of nuclear physiology occur at macromolecular complexes organized on the NM; thus, the topological organization of DNA loops must be important. Here, we describe a general method for determining the structural DNA loop organization in any large genomic region with a known sequence. The method exploits the topological properties of loop DNA attached to the NM and elementary topological principles such as that points in a deformable string (DNA) can be positionally mapped relative to a position-reference invariant (NM), and from such mapping, the configuration of the string in third dimension can be deduced. Therefore, it is possible to determine the specific DNA loop configuration without previous characterization of the LARs involved. We determined in hepatocytes and B-lymphocytes of the rat the DNA loop organization of a genomic region that contains four members of the albumin gene family

EXPERIENCES OF DRUG USERS IN IIA CLASS JAIL YOGYAKARTA

United Nations Office on Drugs and Crime (UNODC) estimated that about 149-272 million people or 3.3 % - 6.1 % of world population aged 15-64 years used drugs (even once) during their life time. This estimation will increase with time (BNN, 2011). The number of prisoners suffering HIV/AIDS in recent years were increasing as well if compared to its numbers in the year 2011 from 787 people to 1042 people. It was estimated that in the year 2015, the number of drug users in Indonesia would increase to 5.8 million people, since the number of drug users at the present time were reached 4 million people. For the time being, in Yogyakarta second A class drug jail , the number of drug users were 256 people; this number were constant; its mean that if there was prisoner got his / her freedom, another prisoner was incoming. Data from BNN in August 2013 years, 70% of 4 million drug users in Indonesia were workers (productive aged). Aim; To discovered population research experiences that cause them used drugs and depend on its. Research method: This was qualitative research with phenomenological approach. Data gathering technique were deep interview and FGD toward 30 respondents. Data were analyzed using reduction, data display, and conclusion drawing/verification. The majority of respondents mentioned that they used drugs because of they wanted to know and the influence of friends. Drugs, kinds of sabu, used to increase energy and ganja were used to obtain peacefulness. Drugs users wanted to use its forever; therefore, they wanted to stop because of punishment to be in jail not because of the drugs had negative effects to the body. The majority of respondents mentioned that to stop using drugs must be self motivated; on the contrary, the obstacle to stop using drugs because of missing sensation to use it. They named it suggest. Using drugs were conducted by research population because of environmental influence, to increase energy and to obtain peacefulness. Keywords : The experiences of drug use

Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome

Bacteria in Permafrost

Significant numbers of viable ancient microorganisms are known to be present within the permafrost. They have been isolated in both polar regions from the cores up to 400 m deep and ground temperatures of -27 C. The age of the cells corresponds to the longevity of the permanently frozen state of the soils, with the oldest cells dating back to {approx}3 million years in the Arctic, and {approx}5 million years in the Antarctic. They are the only life forms known to have retained viability over geological time. Thawing of the permafrost renews their physiological activity and exposes ancient life to modern ecosystems. Thus, the permafrost represents a stable and unique physicochemical complex, which maintains life incomparably longer than any other known habitats. If we take into account the depth of the permafrost layers, it is easy to conclude that they contain a total microbial biomass many times higher than that of the soil cover. This great mass of viable matter is peculiar to permafrost only

Migratory birds along the Mediterranean/Black Sea Flyway as carriers of zoonotic pathogens

At the crossroad between Europe, Asia and Africa, Bulgaria is part of the Mediterranean/Black Sea Flyway (MBSF) used by millions of migratory birds. In this study bird species migrating through Bulgaria were investigated as carriers of zoonotic pathogens. In total, 706 birds belonging to 46 species were checked for the presence of various bacterial pathogens (Campylobacter, Yersinia, Salmonella, Listeria, Escherichia coli, Staphylococcus aureus, Francisella tularensis, Coxiella burnetii, Borrelia burgdorferi and Brucella spp). We detected Campylobacter 16S rDNA gene in 1.3% of birds, but none were pathogenic species. E. coli 16S rDNA gene was found in 8.8% of the birds. Out of 34 birds that transported Y. enterocolitica strains (5.05%), only one carried a pathogenic isolate. Three birds (0.4%) were carriers of non-pathogenic Salmonella strains. Four avian samples (0.6%) were positive for Listeria monocytogenes and one (0.15 %) - for Brucella spp. None of the birds tested carried the tick-borne pathogens C. burnetii or B. burgdorferi s.l. Antibiotic resistant strains were detected, suggesting that migratory birds could be reservoirs and spreaders of bacterial pathogens as well as antibiotic resistance genes.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Synthesis and styrene copolymerization of novel methyl and oxy ring-disubstituted tert-butyl phenylcyanoacrylates

Novel ring-disubstituted tert-butyl phenylcyanoacrylates, RPhCH=C(CN)CO2C(CH3)3, where R is 2,5-dimethyl, 3,4-dimethyl, 2,3-dimethoxy, 2,5-dimethoxy, 3,5-dimethoxy, 4-methoxy-2-methyl, 4-methoxy-3-methyl, 3-ethoxy-4-methoxy, 3-ethoxy-4-hydroxy, 3-ethoxy-2-hydroxy, 3-benzyloxy-4-methoxy, 4-benzyloxy-3-methoxy, 2,3-(methylenedioxy) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and tret-butyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the acrylates were copolymerized with styrene in solution with radical initiation at 70C. The compositions of the copolymers were calculated from nitrogen analysis

Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells

Here, we present DNA aptamers capable of specific binding to glial tumor cells in vitro, ex vivo, and in vivo for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified molecular target proteins of the aptamers by mass spectrometry; the potential binding sites of Gli-233 to the target protein and the role of post-translational modifications were verified by molecular dynamics simulations. The anti-glioma aptamers Gli-233 and Gli-55 were used to detect circulating tumor cells in liquid biopsies. These aptamers were used for in situ, ex vivo tissue staining, histopathological analyses, and fluorescence-guided tumor and PET/CT tumor visualization in mice with xenotransplanted human astrocytoma. The aptamers did not show in vivo toxicity in the preclinical animal study. This study demonstrates the potential applications of aptamers for precise diagnostics and fluorescence-guided surgery of brain tumors.peerReviewe