26 research outputs found

    Human DNA helicase B (HDHB) binds to replication protein A and facilitates cellular recovery from replication stress.

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    Maintenance of genomic stability in proliferating cells depends on a network of proteins that coordinate chromosomal replication with DNA damage responses. Human DNA helicase B (HELB or HDHB) has been implicated in chromosomal replication, but its role in this coordinated network remains undefined. Here we report that cellular exposure to UV irradiation, camptothecin, or hydroxyurea induces accumulation of HDHB on chromatin in a dose- and time-dependent manner, preferentially in S phase cells. Replication stress-induced recruitment of HDHB to chromatin is independent of checkpoint signaling but correlates with the level of replication protein A (RPA) recruited to chromatin. We show using purified proteins that HDHB physically interacts with the N-terminal domain of the RPA 70-kDa subunit (RPA70N). NMR spectroscopy and site-directed mutagenesis reveal that HDHB docks on the same RPA70N surface that recruits S phase checkpoint signaling proteins to chromatin. Consistent with this pattern of recruitment, cells depleted of HDHB display reduced recovery from replication stress

    Primjena umjetnih neuralnih mreža u optimiranju koncentracije viših alkohola u izradi emulzija ulje/voda

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    The purpose of this study was to optimize the concentration of a fatty alcohol, in addition to internal phase concentration, for formulating a stable O/W emulsion, by using artificial neural networks (ANNs). Predictions from ANNs are accurate and allow quantification of the relative importance of the inputs. Furthermore, by varying the network topology and parameters it was possible to obtain output values that were close to experimental values. The ANN model\u27s predictive results and the actual output values were compared. R2 values depict the percentage of response variability for the model; R2 values of 0.84 for the model suggested adequate modeling, which is supported by the correlation coefficient value of 0.9445.Cilj rada bio je pomoću umjetnih neuralnih mreža (ANNs) optimirati koncentraciju viših alkohola kao unutarnje faze za pripravu stabilnih emulzija ulje/voda. Rezultati ANN predviđanja su točni i omogućavaju kvantifikaciju ulaznih parametara. Nadalje, varirajući topologiju mreže i parametre moguće je dobiti izlazne vrijednosti koje su blizu eksperimentalnih vrijednosti. Usporedbom rezultata ANN predviđanja i stvarnih izlaznih vrijednosti dobiveni su visoki koeficijenti korelacije (R2 = 0,84 i r2 = 0,9445)

    Investigation of the Ligand–Nanoparticle Interface: A Cryogenic Approach for Preserving Surface Chemistry

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    Ligand-functionalized nanoparticles have replaced bare nanoparticles from most biological applications. These applications require tight control over size and stability of nanoparticles in aqueous medium. Understanding the mechanism of interaction of nanoparticle surfaces with functional groups of different organic ligands such as carboxylic acids is confounding despite the two decades of research on nanoparticles because of the inability to characterize their surfaces in their immediate environment. Often the surface interaction is understood by correlating the information available, in a piecemeal approach, from surface sensitive spectroscopic information on ligands and the bulk and surface information on nanoparticles. In present study we report the direct interaction of 5–7 nm cerium oxide nanoparticles surface with acetic acid. An in-situ XPS study was carried out by freezing the aqueous solution of nanoparticles to liquid nitrogen temperatures. Analysis of data collected concurrently from the ligands as well as functionalized frozen cerium oxide nanoparticles show that the acetic acid binds to the ceria surface in both dissociated and molecular state with equal population over the surface. The cerium oxide surface was populated predominantly with Ce<sup>4+</sup> ions consistent with the thermal hydrolysis synthesis. DFT calculations reveal that the acetate ions bind more strongly to the cerium oxide nanoparticles as compared to the water molecules and can replace the hydration sphere of nanoparticles resulting in high acetate/acetic surface coverage. These findings reveal molecular level interaction between the nanoparticle surfaces and ligands, giving a better understanding of how materials behave in their immediate solution environment. This study also proposes a simple and elegant methodology to directly study the surface functional groups attached to nanoparticles in their immediate solution environment

    Investigation of Copper(I) Oxide Quantum Dots by Near-Edge X-ray-Absorption Fine-Structure Spectroscopy

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    Copper(I) oxide quantum dots (OQDs) were grown in various thicknesses on different SrTiO3(001) surfaces and were investigated by near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The experimental growth conditions for the OQDs were optimized to obtain Cu2O as the major phase. The OQDs grown on clean SrTiO3(001) surfaces at 825 K and higher with p(O2) of 9.0 Ă— 10-7 Torr or greater contain mostly CuO, contrasting to OQDs grown at 800 K with p(O2) of 7.0 Ă— 10-7 Torr that contain primarily Cu2O. Furthermore, there is a strong interaction between the SrTiO3(001) surface and the first few monolayers of the OQDs, which induces the formation of Cu(II). However, this interaction is mitigated with increasing thickness of OQDs, resulting in the exclusive formation of Cu2O in the topmost layers. The influence of the SrTiO3(001) substrate on the formation of OQDs can be minimized by modifying the substrate surface using chemical treatment and/or energetic Au2+ ion-beam irradiation. Examination of the photochemical properties of these OQDs shows that prolonged soft X-ray irradiation under vacuum reduces Cu(II), which is present as a minor impurity in the Cu(I) OQDs

    Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase

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    DNA replication requires priming of DNA templates by enzymes known as primases. Although DNA primase structures are available from archaea and bacteria, the mechanism of DNA priming in higher eukaryotes remains poorly understood in large part due to the absence of the structure of the unique, highly conserved C-terminal regulatory domain of the large subunit (p58C). Here, we present the structure of this domain determined to 1.7-Å resolution by X-ray crystallography. The p58C structure reveals a novel arrangement of an evolutionarily conserved 4Fe-4S cluster buried deeply within the protein core and is not similar to any known protein structure. Analysis of the binding of DNA to p58C by fluorescence anisotropy measurements revealed a strong preference for ss/dsDNA junction substrates. This approach was combined with site-directed mutagenesis to confirm that the binding of DNA occurs to a distinctively basic surface on p58C. A specific interaction of p58C with the C-terminal domain of the intermediate subunit of replication protein A (RPA32C) was identified and characterized by isothermal titration calorimetry and NMR. Restraints from NMR experiments were used to drive computational docking of the two domains and generate a model of the p58C–RPA32C complex. Together, our results explain functional defects in human DNA primase mutants and provide insights into primosome loading on RPA-coated ssDNA and regulation of primase activity
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