161 research outputs found
The minor groove-binding agent ELB-21 forms multiple interstrand and intrastrand covalent cross-links with duplex DNA and displays potent bactericidal activity against methicillin-resistant Staphylococcus aureus
No full textObjectives The antistaphylococcal pyrrolobenzodiazepine dimer ELB-21 forms multiple adducts with duplex DNA through covalent interactions with appropriately spaced guanine residues; it is now known to form interstrand and intrastrand adducts with oligonucleotide sequences of variable length. We determined the DNA sequence preferences of ELB-21 in relation to its capacity to exert a bactericidal effect by damaging DNA.Methods Formation of adducts by ELB-21 and 12- to 14-mer DNA duplexes was investigated using ion-pair reversed phase liquid chromatography and mass spectrometry. Drug-induced changes in gene expression were measured in prophage-free Staphylococcus aureus RN4220 by microarray analysis.Results ELB-21 preferentially formed intrastrand adducts with guanines separated by three nucleotide base pairs. Interstrand and intrastrand adducts were formed with duplexes both longer and shorter than the preferred target sequences. ELB-21 elicited rapid bactericidal effects against prophage-carrying and prophage-free S. aureus strains; cell lysis occurred following activation and release of resident prophages. Killing appeared to be due to irreparable damage to bacterial DNA and susceptibility to ELB-21 was governed by the capacity of staphylococci to repair DNA lesions through induction of the SOS DNA damage response mediated by the RecA-LexA pathway.Conclusions The data support the contention that ELB-21 arrests DNA replication, eliciting formation of ssDNA-RecA filaments that inactivate LexA, the SOS repressor, and phage repressors such as Cl, resulting in activation of the DNA damage response and de-repression of resident prophages. Above the MIC threshold, DNA repair is ineffective
Mutation and expression changes in <i>lexA</i> and <i>yneA</i>.
No full text(A) Mutation in lexA (P25L) observed in lineage 2 is physically close to active binding site of LexA protein to DNA (here shown for one of the monomers). The protein structure was obtained from the Protein Data Bank RCSB PDB [103] (https://www.rcsb.org/3d-view/3k3r). Expression of (B) lexA and (C) yneA in ancestral and evolved populations over colony growth cycle: day 1 (blue) to day 7 (red). Bars show average expression (n = 3). Statistics show two-sided Mann Whitney U test, and p-values are adjusted for multiple testing using Benjamini–Hochberg procedure. Source data can be found in S4 and S5 Data. (TIF)</p
Clp-dependent proteolysis of the LexA N-terminal domain in Staphylococcus aureus
No full textThe SOS response is governed by the transcriptional regulator LexA and is elicited in many bacterial species in response to DNA damaging conditions. Induction of the SOS response is mediated by autocleavage of the LexA repressor resulting in a C-terminal dimerization domain (CTD) and an N-terminal DNA-binding domain (NTD) known to retain some DNA-binding activity. The proteases responsible for degrading the LexA domains have been identified in Escherichia coli as ClpXP and Lon. Here, we show that in the human and animal pathogen Staphylococcus aureus, the ClpXP and ClpCP proteases contribute to degradation of the NTD and to a lesser degree the CTD. In the absence of the proteolytic subunit, ClpP, or one or both of the Clp ATPases, ClpX and ClpC, the LexA domains were stabilized after autocleavage. Production of a stabilized variant of the NTD interfered with mitomycin-mediated induction of sosA expression while leaving lexA unaffected, and also significantly reduced SOS-induced mutagenesis. Our results show that sequential proteolysis of LexA is conserved in S. aureus and that the NTD may differentially regulate a subset of genes in the SOS regulon
SOS filamentation causes strongly advanced colony expansion in <i>lexA</i> knockout mutant.
No full text(A) Colony expansion and (B) colony composition in (C) lexA and yneA mutants in week 5 to 7 of the evolution experiment in lineage 2. The lexA knockout mutation in week 6 leads to SOS filamentation, mediated by the expression of yneA that inhibits cell division. Colony expansion is reduced in yneA mutant that appears in week 7, suggesting that SOS filamentation largely explains the strongly improved colony expansion rate in week 6. Since there is no selective benefit for the yneA mutation, as it harms colony spreading, it does not fixate in the population. For figure legend, see caption of Fig 2. Source data can be found in S1 and S2 Data. (TIF)</p
Study of the floodplain of the municipality of Líšnice on the Divoká River
No full textDiplomová práce se zaměřuje na studii záplavového území obce Líšnice na toku řeky Divoká Orlice. Hlavním cílem práce je určit průběh hladin povodňových průtoků v dané lokalitě a navrhnout a posoudit nezbytná protipovodňová opatření. Pro analýzu byl použit 2D matematický model v programu HEC-RAS, který umožnil simulaci povodňových scénářů a výpočet průběhů hladin a hloubek vody. Výsledkem jsou grafické výstupy, které zobrazují průběhy hladin a hloubek vody pro různé povodňové průtoky, a zároveň je navrženo několik protipovodňových opatření. Výsledky této studie mohou sloužit jako podklad pro implementaci těchto opatření a zlepšení ochrany obce Líšnice před povodněmi.The diploma thesis focuses on the floodplain study of the municipality of Lišnice on the Divoká Orlice River. The main goal of the thesis is to determine the flood level profiles for flood discharge scenarios in the area and to design and assess necessary flood protection measures. A 2D mathematical model using the HEC-RAS program was used for the analysis, allowing the simulation of flood scenarios and the calculation of water level and depth profiles. The results include graphical outputs showing the water level and depth profiles for various flood discharges, and several flood protection measures are also proposed. The results of this study can serve as a basis for the implementation of these measures and for improving the flood protection of the Líšnice municipality
p53 9aaTADs activate transcription as small peptides.
No full textThe predicted 9aaTADs in p53 from different species were tested for activation of transcription in LexA hybrid constructs. Similarity of p53 with Gal4 and Sox18 are highlighted. The construct 9p53, labelled with asterisk, has lower expression level compared with other constructs (S1 Fig). Animal picture from Flickr: Lowland Streaked Tenrec, Mantadia, Madagascar, Author: Frank Vassen; Elephant, Author: Jon Mountjoy; Igel (Hedgehog), Author: Mi chaela. All pictures have Creative Commons Attribution 2.0 Generic license.</p
Quadruplex Detection in DNA Sequences
No full textThis master's thesis focuses on search for sequences potentially forming quadruplexes in DNA sequences, their visualization and filtration. For this purpose a web application was created in cooperation with the Institute of biophysics of Academy of science of Czech republic. This application uses a newly created algorithm able to find all possible formations of quadruplex within given input sequence. Design and implementation of this algorithm are also part of this thesis
On Banach-Tarski paradoxical decompositions
No full textIn this thesis, we examine the various paradoxes in all their diversity. We begin by introducing the reader to paradoxes concerning infinity and its basic arithmetic. We then introduce several geometric and algebraic paradoxes that arise from seemingly contradic- tory decompositions. The paper makes extensive use of the notion of equidecomposability and examines its properties in detail. We conclude by comparing it with scissor congru- ence and clarifying the differences between them. The reader will also learn the necessary background information from measure theory and algebra, which are key areas for finding the free subgroup generating paradoxical decompositions. The final section is devoted to the main topic of the paper, the Banach-Tarski paradox, where several propositions are proved and the operation of this paradox in various dimensions is briefly examined.
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