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Search Results: 1 - 10 of 15899 matches for " Jan Mrázek "
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Investigating the Interplay between Nucleoid-Associated Proteins, DNA Curvature, and CRISPR Elements Using Comparative Genomics
Hao Tong, Jan Mrázek
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0090940
Abstract: Many prokaryotic and eukaryotic genomes feature a characteristic periodic signal in distribution of short runs of A or T (A-tracts) phased with the DNA helical period of ~10–11 bp. Such periodic spacing of A-tracts has been associated with intrinsic DNA curvature. In eukaryotes, this periodicity is a major component of the nucleosome positioning signal but its physiological role in prokaryotes is not clear. One hypothesis centers on possible role of intrinsic DNA bends in nucleoid compaction. We use comparative genomics to investigate possible relationship between the A-tract periodicity and nucleoid-associated proteins in prokaryotes. We found that genomes with DNA-bridging proteins tend to exhibit stronger A-tract periodicity, presumably indicative of more prevalent intrinsic DNA curvature. A weaker relationship was detected for nucleoid-associated proteins that do not form DNA bridges. We consider these results an indication that intrinsic DNA curvature acts collaboratively with DNA-bridging proteins in maintaining the compact structure of the nucleoid, and that previously observed differences among prokaryotic genomes in terms DNA curvature-related sequence periodicity may reflect differences in nucleoid organization. We subsequently investigated the relationship between A-tract periodicity and presence of CRISPR elements and we found that genomes with CRISPR tend to have stronger A-tract periodicity. This result is consistent with our earlier hypothesis that extensive A-tract periodicity could help protect the chromosome against integration of prophages, possibly due to its role in compaction of the nucleoid.
PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences
Jan Mrázek, Tejas Chaudhari, Aryabrata Basu
Microbial Informatics and Experimentation , 2011, DOI: 10.1186/2042-5783-1-13
Abstract: We present novel tools suitable for assessments of DNA curvature-related sequence periodicity in nucleotide sequences at the genome scale. Utility of the present software is demonstrated on a comparison of sequence periodicities in the genomes of Haemophilus influenzae, Methanocaldococcus jannaschii, Saccharomyces cerevisiae, and Arabidopsis thaliana. The software can be accessed through a web interface and the programs are also available for download.The present software is suitable for comparing DNA curvature-related sequence periodicity among different genomes as well as for analysis of intrachromosomal heterogeneity of the sequence periodicity. It provides a quick and convenient way to detect anomalous regions of chromosomes that could have unusual structural and functional properties and/or distinct evolutionary history.Most naturally occurring DNA sequences feature two strong periodic patterns. The first relates to a 3 bp period resulting from amino acid and codon usage biases in protein coding genes. The second arises from periodic spacing of A-tracts (short runs of A or T) phased with the DNA helical period of ~10.5 bp. The periodically spaced A-tracts are a primary indicator of intrinsically bent DNA and the main component of nucleosome positioning signals in eukaryotes [1-3]. Similar periodic patterns are present in prokaryotes, where they could contribute to DNA packaging in the nucleoid [4,5], promote the appropriate mode of supercoiling [6,7], and/or facilitate the initiation and termination of transcription [8,9]. There are significant differences in the character and intensity of these periodic patterns among different genomes as well as among different segments of the same genome [4,6,7,10]. In some species, the intragenomic heterogeneity of the sequence periodicity has been linked to local variance in gene expression and chromatin structure [4,11,12].Despite the biological significance of DNA curvature-related sequence periodicity, there are virtual
Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families
Anuj Srivastava,Liming Cai,Jan Mrázek,Russell L. Malmberg
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0020484
Abstract: The goal of this work was to study mutational patterns in the evolution of RNA secondary structure. We analyzed bacterial tmRNA, RNaseP and eukaryotic telomerase RNA secondary structures, mapping structural variability onto phylogenetic trees constructed primarily from rRNA sequences. We found that secondary structures evolve both by whole stem insertion/deletion, and by mutations that create or disrupt stem base pairing. We analyzed the evolution of stem lengths and constructed substitution matrices describing the changes responsible for the variation in the RNA stem length. In addition, we used principal component analysis of the stem length data to determine the most variable stems in different families of RNA. This data provides new insights into the evolution of RNA secondary structures and patterns of variation in the lengths of double helical regions of RNA molecules. Our findings will facilitate design of improved mutational models for RNA structure evolution.
The zinc-ribbon domain of Helicobacter pylori HP0958: requirement for RpoN accumulation and possible roles of homologs in other bacteria
Lara E Pereira, Jennifer Tsang, Jan Mrázek, Timothy R Hoover
Microbial Informatics and Experimentation , 2011, DOI: 10.1186/2042-5783-1-8
Abstract: Levels of RpoN were greatly reduced in H. pylori strains that expressed the FlgZC202S or FlgZC223S variants. The FlgZC202S variant, but not the FlgZC223S variant, accumulated at levels similar to the wild-type protein. DUF164 proteins are not universally distributed and appear to be absent in several major bacterial taxa, including Cyanobacteria as well as Alpha-, Beta- and Gammaproteobacteria. With the exception of the Actinobacteria, members of which generally lack RpoN, genes encoding DUF164 proteins and RpoN are frequently found in the same genome. Interestingly, many of the DUF164 proteins in Actinobacteria and Bacteroidetes lack most or even all of the conserved cysteine residues.These findings suggest the importance of the zinc-ribbon domain of FlgZ in protecting RpoN from turnover. Since many bacteria that possess a DUF164 protein also contain RpoN, DUF164 proteins may have roles in RpoN protection or function in other bacteria.Helicobacter pylori is a member of the Epsilonproteobacteria that colonizes the human gastric mucosa where it causes a variety of gastrointestinal diseases, including acute gastritis, peptic and duodenal ulcers, B cell MALT lymphoma, and gastric adenocarcinoma [1-3]. Colonization of the gastric mucosa by H. pylori requires the bacterium to be motile [4,5], which is achieved through a cluster of polar sheathed flagella.The bacterial flagellum is a complex structure consisting of three basic substructures - the basal body, hook and filament. Dozens of genes are required for flagellar biogenesis and the expression of these genes is regulated by a transcriptional hierarchy in which genes are expressed as their products are needed for assembly [6,7]. All three of the RNA polymerase sigma (σ) factors in H. pylori are involved in flagellar biogenesis. In general, genes needed early in flagellar assembly are under control of the primary σ factor RpoD (σ80), while RpoN (σ54) is responsible for transcription of genes needed midway through flage
Introduction
Harry A. Poeze,Rudolf Mrázek
Bijdragen tot de Taal-, Land- en Volkenkunde , 1994,
Abstract:
Responses of Vegetation Stages with Woody Dominants to Stress and Disturbance During Succession on Abandoned Tailings in Cultural Landscape
Pavel Ková , Michal tefánek, Jakub Mrázek
Journal of Landscape Ecology , 2011, DOI: 10.2478/v10285-012-0037-9
Abstract: Studies of ecological succession on tailing containments (abandoned sedimentation basins with waste deposited by a factory producing sulphuric acid from pyrite ore) near the village of Chvaletice (Eastern Bohemia, Czech Republic) were carried out since 1973 with increased intensity and complexity between 1986 and 2002 (Ková 2004). Vegetation cover in its relationships to various factors has been periodically monitored up to now. The abandoned ore-washery deposit is characterized by relative strong toxicity of the sediment material (high heavy metal content) and fluctuations of the microsite conditions up to extreme values (pH, salinity, surface temperatures). Species richness and the courses of some ecological processes are influenced both by availability of plant diaspores (regional species pool) determined with the presence of adequate dispersal mechanisms (anemochory, zoochory) and by the seasonal moderation of environmental variables excluding stress non-tolerant species at extreme epizodes and enabling survival of resistant species during the competition. Long lasting existence of patches without any vegetation together with herbaceous types of stands and woody successional stages create mosaics on the surface plateau. The oldest tree stands (in average 20 - 30 years old) are predominantly formed by Populus tremula and Betula pendula, with minor admixture of Salix sp. div. (mainly S. caprea), Pinus sylvestris, Quercus robur or Cerassus avium, rarely Sarothamnus scoparius. The abundance ratio of two main dominants, aspen and birch, was changed for the benefit of the first one after the summer fire in extremely hot days. The effect of clonality on aspen regeneration and regrowth immediately after the fire disturbance was profitably manifested and it apparently facilitates the present state with aspen prevailing in the most forested tailing places at present, seventeen years after the fire. This fact supports the importance of clonal plant species role during primary succession.
Coronary versus carotid blood flow and coronary perfusion pressure in a pig model of prolonged cardiac arrest treated by different modes of venoarterial ECMO and intraaortic balloon counterpulsation
Jan Bělohlávek, Mikulá? Ml?ek, Michal Huptych, Tomá? Svoboda, ?těpán Havránek, Petr O?t'ádal, Tomá? Bou?ek, Tomá? Kovárník, Franti?ek Mlejnsky, Vratislav Mrázek, Marek Bělohlávek, Michael Aschermann, Ale? Linhart, Otomar Kittnar
Critical Care , 2012, DOI: 10.1186/cc11254
Abstract: In 11 female pigs (50.3 ± 3.4 kg), CA was randomly treated by FF versus FS ECMO ± IABP. Animals under general anesthesia had undergone 15 minutes of ventricular fibrillation (VF) with ECMO flow of 5 to 10 mL/kg/min simulating low-flow CA followed by continued VF with ECMO flow of 100 mL/kg/min. CaBF and CoBF were measured by a Doppler flow wire, cerebral and peripheral oxygenation by near infrared spectroscopy. CoPP, myocardial oxygen metabolism and resuscitability were determined.CaBF reached values > 80% of baseline in all regimens. CoBF > 80% was reached only by the FF ECMO, 90.0% (66.1, 98.6). Addition of IABP to FF ECMO decreased CoBF to 60.7% (55.1, 86.2) of baseline, P = 0.004. FS ECMO produced 70.0% (49.1, 113.2) of baseline CoBF, significantly lower than FF, P = 0.039. Addition of IABP to FS did not change the CoBF; however, it provided significantly higher flow, 76.7% (71.9, 111.2) of baseline, compared to FF + IABP, P = 0.026. Both brain and peripheral regional oxygen saturations decreased after induction of CA to 23% (15.0, 32.3) and 34% (23.5, 34.0), respectively, and normalized after ECMO institution. For brain saturations, all regimens reached values exceeding 80% of baseline, none of the comparisons between respective treatment approaches differed significantly. After a decline to 15 mmHg (9.5, 20.8) during CA, CoPP gradually rose with time to 68 mmHg (43.3, 84.0), P = 0 .003, with best recovery on FF ECMO. Resuscitability of the animals was high, both 5 and 60 minutes return of spontaneous circulation occured in eight animals (73%).In a pig model of CA, both FF and FS ECMO assure adequate brain perfusion and oxygenation. FF ECMO offers better CoBF than FS ECMO. Addition of IABP to FF ECMO worsens CoBF. FF ECMO, more than FS ECMO, increases CoPP over time.A venoarterial (VA) extracorporeal membrane oxygenation (ECMO) based approach is used for urgent hemodynamic stabilization in patients with profound cardiogenic shock and, increasingly, also in card
Plasma xenin concentrations in children
Beata Mrózek,Przemys?aw J. Tomasik,Andrzej W?drychowicz,Ma?gorzata Wójcik
Pediatric Endocrinology, Diabetes and Metabolism , 2012,
Abstract: Introduction: Xenin is a newly discovered peptide in humans. The concentration of xenin in human plasma increases after meals and therefore this peptide is considered as a marker of satiety. The mechanism of xenin action in humans has not been thoroughly examined. MEDLINE database contains only few reports about the role of xenin in adults and none of them were performed in children. Aim of the study: The aim of the study was to evaluate the concentration of xenin in children with energy balance disorders. Material and methods: Plasma xenin concentration was measured in children with inflammatory bowel syndrome (IBD) (n=53; age 14±3 years) before, during and after treatment, obese children (n=26; age 14±2.8 years) during the OGGT test and in healthy children (n=10; age 15.7±2.2 years). Xenin was determined in the plasma using the radioimmunological method. Results: The mean plasma xenin concentration in the healthy children was 371±36 pg/ml. In the children with an acute phase of IBD the mean concentration of xenin was 367±96 pg/ml and an increase during the treatment to the mean value 399±55 pg/ml was noted. The highest mean value of xenin concentration (412±55 pg/ml) was found during early remission. In obese children, the mean concentration of xenin (198±69 pg/ml) was significantly lower as compared to children with IBD and to control (p<0.001 in both cases). The glucose load did not have any effect on xenin concentration in obese children. Conclusions: Xenin takes part in the regulation of energy balance in children.
Microwave saturation spectroscopy of nitrogen-vacancy ensembles in diamond
P. Kehayias,M. Mrózek,V. M. Acosta,A. Jarmola,D. S. Rudnicki,R. Folman,W. Gawlik,D. Budker
Physics , 2014, DOI: 10.1103/PhysRevB.89.245202
Abstract: Negatively-charged nitrogen-vacancy (NV$^-$) centers in diamond have generated much recent interest for their use in sensing. The sensitivity improves when the NV ground-state microwave transitions are narrow, but these transitions suffer from inhomogeneous broadening, especially in high-density NV ensembles. To better understand and remove the sources of broadening, we demonstrate room-temperature spectral "hole burning" of the NV ground-state transitions. We find that hole burning removes the broadening caused by magnetic fields from $^{13}$C nuclei and demonstrate that it can be used for magnetic-field-insensitive thermometry.
THE FIRST LONG WOVELS IN THE DIALECT OF ARAPK R/MALATYA ARAPK R/MALATYA A ZINDA B R NC L UZUN üNLüLER
Fatih ?ZEK
Turkish Studies , 2009,
Abstract: The fact that the first long wovels are shortened in the Oguz Turkish dialects expect Turkmen Turkish is the most common thought. In the standart Turkey Turkish the first long wovels are also shortened. However, the studies which started in the second half of the twentieth century and the studies Turkey Turkish has been preserved even if it is rare. These studies are very important beacuse they are seen in the Oguz Turkish dialect group except Turkmen Turkish. Our study comprises of the Arapkir town of the province Malatya. We found out some words with the first long wovel in the studies we did in this area. We made a list of these words that we found in the conclusion part of our study. O uz grubu Türk leh elerinde, Türkmen Türk esi d nda, birincil uzun ünlülerin normal süreli kar l klar na d nü erek k sald yayg n bir kanaattir. Türkiye Türk esi l ünlü dilinde de birincil uzun ünlüler tamamen k salm t r. Ancak 20. yüzy l n ikinci yar s nda ba layan ve son zamanlarda yo unluk kazanan al malar Türkiye Türk esi l ünlü diline kaynakl k eden Türkiye Türk esi a zlar nda birincil uzun ünlülerin da n k da olsa korundu unu g stermektedir. Bu al malar Türkmen Türk esi d nda, birincil uzun ünlülerin O uz grubu Türk leh elerinde g rülmesi bak m ndan son derece nemlidir. al mam z Malatya ilinin Arapkir il esini kapsamaktad r. Bu b lgede yapt m z a z derlemelerinde birincil uzun ünlülü baz kelimeler tespit ettik. Türkiye Türk esi a zlar nda birincil uzun ünlülerin bulunmas bak m ndan nemli olan bu kelimeleri al mam z n sonunda bir liste halinde verdik.
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