Cruciform structures are a common DNA feature important for regulating biological processes

DNA cruciforms play an important role in the regulation of natural processes involving DNA. These structures are formed by inverted repeats, and their stability is enhanced by DNA supercoiling. Cruciform structures are fundamentally important for a wide range of biological processes, including replication, regulation of gene expression, nucleosome structure and recombination. They also have been implicated in the evolution and development of diseases including cancer, Werner's syndrome and others

A Comparison of Curricular Materials in Regards to the Teaching of Civics in the Czech Republic and in the USA

Cílem této diplomové práce bylo srovnání kurikulárních dokumentů vztahujících se ke vzdělávací oblasti Člověk a společnost v ČR a Společenské vědy v USA. Dokumenty jsem porovnávala na různé úrovni obecnosti, od legislativního zakotvení až po jednotlivé školní vzdělávací programy. Každá tato úroveň je specifická a zabývá se problematikou z jiného úhlu, přesto lze vysledovat určité tendence, specifické pro dokumenty obou zemí: V USA jde o důraz na praktičnost a použitelnost dokumentu, přesně specifikuje, co je jeho smyslem a snaží se o maximální srozumitelnost. České dokumenty mívají někdy tendenci sklouznout do obecných prohlášení, ze kterých pro praxi nic nevyplývá, a na svého čtenáře klást vysoké nároky co se týče jejich srozumitelnosti. Americké dokumenty, ač nejsou psané mou mateřštinou, nevyžadovaly druhé přečtení pochopení toho, co vlastně deklarují. V této zamlženosti českých dokumentů vidím jeden ze zdrojů problémů, které přináší implementace reformy školství v České republice. Přestože dílčí cíle reforem obou zemí se liší, hlavní cíl zůstává stejný: Zajistit svým občanům co nej lepší možné vzdělání. Přestože se obě reformy potýkají s vlastními problémy, směřování obou je podle mého názoru v zásadě dobré, je jen třeba nezastavit se na půli cesty a pokračovat v práci na těch oblastech, které potřebují...This diploma thesis is a comparative study of Czech and American curricular documents concerning the educational reform that is taking place both in the Czech Republic and the United States of America. By comparing the documents I have tried to find strengths and weaknesses of both reforms and educational systems in general and suggest some means of improvements in areas where I found it useful. I was comparing the documents on more different levels: In the first chapter I was concentrating on two acts as the bases of the educational reforms: No Child Left Behind in the USA and Národní program rozvoje vzdělávání v České republice [National program of educational development in the Czech Republic] in the Czech Republic. The second chapter is dealing with the national curricular frameworks, and is comparing the Czech national framework to Michigan Curriculum Framework. The third chapter is concerned with schools' own curricula, and with the recommended ways how to develop them in both countries. As this thesis is aimed at area social studies and at civic education particularly, the next chapter compares the content standards and benchmarks of both frameworks. In the practical part of this diploma thesis I described the project that I carried out at middle school Vinařská in Ústí nad Labem in the Czech...Katedra občanské výchovy a filosofiePedagogická fakultaFaculty of Educatio

In silico analyses of p53-REs ranked by p73 transcription activation (TA ratio) compared to empty vector.

<p>Bases which form an inverted repeat are in bold. The presence of inverted repeats was analyzed by Palindrome finder [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195835#pone.0195835.ref038" target="_blank">38</a>] with parameters 7-10/0-10/0-1 (<b>L</b>ength/<b>S</b>pacer/<b>M</b>ismatch). CF rank in the same format is shown in the last column. TA ratios were derived from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195835#pone.0195835.ref032" target="_blank">32</a>].</p

Comparison of the p73 transactivation ratio in sequences without (left) and with (right) inverted repeats–a box plot (data from Table 1).

<p>Comparison by Wilcoxon rank test with continuity correction show significantly higher values for the selection with the inverted repeats at target sites (p<0.01), marked with an asterisk.</p

Comparison of p53 and p73 transactivation in yeast.

<p>Three isogenic yeast strains were used, two with p53 targets sites (XA and XG) and one without a p53 target site (FLT) upstream of the luciferase gene. Cells containing pTSG-p53 (p53, left), pTSG-p73 (p73, middle) or pTSG with no insert (empty, right) were treated with galactose to induce p53 or p73 from the <i>GAL1</i> promoter. The histogram plots average luminescence and standard deviations of three biological replicates. Asterisks indicate a significant induction of p53 or p73-dependent transactivation (p<0.05). The sequences of the XA and XG constructs are shown in their potential cruciform structures.</p

p73-dependent transactivation potential in yeast.

<p>p73 protein was expressed from pTSG-p73 under an inducible <i>GAL1</i> promoter. The indicated reporter yeast strains were also transformed with an empty pTSG vector and reporter activity was normalized to cell numbers and plotted as fold induction over empty vector. Average luminescence and standard deviations of three biological replicates are shown. For each strain, luciferase activity was measured at 6 hours of culture in media in the absence of galactose (black) or after induction of p73 with two different concentrations of galactose to induce different levels of p73 (0.008% galactose, white; 0.032% galactose, streaked). Asterisks indicate significant induction of p73-dependent transactivation at each galactose level (p<0.05). RE sequences are shown below each set of conditions.</p

Models of cruciform structure formation in p53 target sequences.

<p>Using mfold software we analyzed the structure and dG of the indicated p53 target sequences with potential to form cruciform structure (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195835#pone.0195835.t001" target="_blank">Table 1</a>). GC bonds are shown in red, AT bonds in blue and mismatched GT bonds in green.</p

IFI16 Preferentially Binds to DNA with Quadruplex Structure and Enhances DNA Quadruplex Formation.

Interferon-inducible protein 16 (IFI16) is a member of the HIN-200 protein family, containing two HIN domains and one PYRIN domain. IFI16 acts as a sensor of viral and bacterial DNA and is important for innate immune responses. IFI16 binds DNA and binding has been described to be DNA length-dependent, but a preference for supercoiled DNA has also been demonstrated. Here we report a specific preference of IFI16 for binding to quadruplex DNA compared to other DNA structures. IFI16 binds to quadruplex DNA with significantly higher affinity than to the same sequence in double stranded DNA. By circular dichroism (CD) spectroscopy we also demonstrated the ability of IFI16 to stabilize quadruplex structures with quadruplex-forming oligonucleotides derived from human telomere (HTEL) sequences and the MYC promotor. A novel H/D exchange mass spectrometry approach was developed to assess protein interactions with quadruplex DNA. Quadruplex DNA changed the IFI16 deuteration profile in parts of the PYRIN domain (aa 0-80) and in structurally identical parts of both HIN domains (aa 271-302 and aa 586-617) compared to single stranded or double stranded DNAs, supporting the preferential affinity of IFI16 for structured DNA. Our results reveal the importance of quadruplex DNA structure in IFI16 binding and improve our understanding of how IFI16 senses DNA. IFI16 selectivity for quadruplex structure provides a mechanistic framework for IFI16 in immunity and cellular processes including DNA damage responses and cell proliferation