Transcription factor-dependent loading of the E1 initiator reveals modular assembly of the papillomavirus origin melting complex

Replication of bovine papillomavirus type 1 DNA absolutely requires the viral transcription factor E2 as well as the initiator Fl, although Fl alone has all the activities expected of an initiator protein. El assembles on the DNA in a stepwise fashion and undergoes a transition in activities from site-specific DNA-binding protein to mobile helicase. Complex assembly is assisted by the viral transcription factor E2 at two levels. E2 acts generally as a specificity factor, which through cooperative binding with El generates an initial Fl complex containing three Fl dimers bound to ori on one face of the DNA, El-ori. Furthermore, E2 can promote the transition to an ori melting complex by recruiting additional Fl molecules to ori, effectively reducing the Fl concentration required for ori melting. This reaction is dependent on an Ea-binding site positioned distal to the precursor E1-ori complex. The final origin melting complex has two subunits that each encircle the DNA and function independently to melt ori. The assembly pathway we describe has implication for understanding DNA melting and unwinding reactions, which are generally poorly understood

System size and beam energy dependence of azimuthal anisotropy from PHENIX

We present azimuthal anisotropy measurements in Au+Au and Cu+Cu collisions at $\sqrt{s_{NN}}$ = 62.4 and 200 GeV. Comparison between reaction plane and cumulant $v_2$ measurements in Au+Au collisions at $\sqrt{s_{NN}}$ = 200 GeV show that non-flow contributions, originating mainly from jets, influence the extracted $v_2$ for $p_T$ $\gtrsim$ 3.5 GeV/c. Number of constituent quark (NCQ) scaling of $v_2$, when studied as a function of transverse kinetic energy $KE_T$, is seen to hold for Au+Au collisions at $\sqrt{s_{NN}}$ = 62.4 and 200 GeV and for Cu+Cu collisions at $\sqrt{s_{NN}}$ = 200 GeV for $KE_{T}$ $\lesssim$ 1 GeV/c. Differential hexadecupole flow $v_4$ seems to exhibit scaling with integral $v_2$ for centrality $\le$ 40% as has been observed for differential $v_2$.Comment: 4 pages, 3 figures, Proceedings of the QM2008 Conference, Jaipur, India February 4-10 200

Measurements of Cold Nuclear Matter Effects on J/psi in the PHENIX Experiment via Deuteron-Gold Collisions

A new calculation of R_{dAu} has been performed using the 2003 d+Au data and the higher-statistics 2005 p+p data. These nuclear modification factors are compared to calculations using nuclear-modified PDFs and a J/psi breakup cross section is extracted. These values are then used to project the cold nuclear matter effects in Au+Au collisions. Additionally, a more data-driven projection is performed.Comment: 4 pages, 6 figures, proceedings for Quark Matter 200

Specific recognition nucleotides and their DNA context determine the affinity of E2 protein for 17 binding sites in the BPV-1 genome

The DNA context of nucleotides that a protein recognizes can influence the strength of the protein-DNA interaction. Moreover, in prokaryotes, understanding the quantitative differences in binding affinities that result in part from the DNA context is often important in describing regulatory mechanisms. Nevertheless, these issues have not been a major focus yet for the investigation of protein-DNA interactions in eukaryotes. In this study, we explored the binding specificity and the range of affinities that the BPV-1 E2 transcriptional activator has for DNA. Because E2 binding sites are positioned near several different BPV-1 promoters, such quantitative information may be important to understand transcriptional regulatory mechanisms in BPV-1. Gel retardation assays and DNA footprinting were used to quantitate the affinities of the E2 binding sites in the viral genome. In the process, five sites were discovered, which, on the basis of sequence, had not been predicted previously to interact with the E2 protein. Equilibrium and kinetic studies show that the range of E2 affinities of the 17 sites varied over 300-fold. The sequence elements responsible for E2 recognition of DNA were determined by missing contact analysis of several sites and a point mutation analysis of one site. The results presented show that the affinity of an E2 binding site is to a large extent determined by the availability of specific contacts, but the data also strongly suggest that DNA structure plays an important role

Peculiarities in produced particles emission in 208Pb + Ag(Br) interactions at 158 A GeV/c

The angular structures of particles produced in 208Pb induced collisions with Ag(Br) nuclei in an emulsion detector at 158 A GeV/c have been investigated. Nonstatistical ring-like substructures in azimuthal plane of the collision have been found and their parameters have been determined. The indication on the formation of the ring-like substructures from two symmetrical emission cones - one in the forward and other in the backward direction in the center-of mass system have been obtained. The ring-like substructures parameters have been determined. The experimental results are in an agreement with I.M. Dremin idea, that mechanism of the ring-like substructures formation in nuclear collisions is similar to that of Cherenkov electromagnetic radiation.Comment: 10 pages, 7 figures, Report at the HADRON STRUCTURE'04 Conference, Smolenice, Slovakia, 30.8.-3.9.200

The eukaryotic leading and lagging strand DNA polymerases are loaded onto primer-ends via separate mechanisms but have comparable processivity in the presence of PCNA

Saccharomyces cerevisiae DNA polymerase δ (Pol δ) and DNA polymerase ε (Pol ε) are replicative DNA polymerases at the replication fork. Both enzymes are stimulated by PCNA, although to different levels. To understand why and to explore the interaction with PCNA, we compared Pol δ and Pol ε in physical interactions with PCNA and nucleic acids (with or without RPA), and in functional assays measuring activity and processivity. Using surface plasmon resonance technique, we show that Pol ε has a high affinity for DNA, but a low affinity for PCNA. In contrast, Pol δ has a low affinity for DNA and a high affinity for PCNA. The true processivity of Pol δ and Pol ε was measured for the first time in the presence of RPA, PCNA and RFC on single-stranded DNA. Remarkably, in the presence of PCNA, the processivity of Pol δ and Pol ε on RPA-coated DNA is comparable. Finally, more PCNA molecules were found on the template after it was replicated by Pol ε when compared to Pol δ. We conclude that Pol ε and Pol δ exhibit comparable processivity, but are loaded on the primer-end via different mechanisms

A DNA-binding activity in BPV initiator protein E1 required for melting duplex ori DNA but not processive helicase activity initiated on partially single-stranded DNA

The papillomavirus replication protein E1 assembles on the viral origin of replication (ori) as a series of complexes. It has been proposed that the ori DNA is first melted by a head-to-tail double trimer of E1 that evolves into two hexamers that encircle and unwind DNA bi-directionally. Here the role of a conserved lysine residue in the smaller tier or collar of the E1 helicase domain in ori processing is described. Unlike the residues of the AAA+ domain DNA-binding segments (β-hairpin and hydrophobic loop; larger tier), this residue functions in the initial melting of duplex ori DNA but not in the processive DNA unwinding of partially single-stranded test substrates. These data therefore define a new DNA-binding related activity in the E1 protein and demonstrate that separate functional elements for DNA melting and helicase activity can be distinguished. New insights into the mechanism of ori melting are elaborated, suggesting the coordinated involvement of rigid and flexible DNA-binding components in E1

From limit cycles to strange attractors

We define a quantitative notion of shear for limit cycles of flows. We prove that strange attractors and SRB measures emerge when systems exhibiting limit cycles with sufficient shear are subjected to periodic pulsatile drives. The strange attractors possess a number of precisely-defined dynamical properties that together imply chaos that is both sustained in time and physically observable.Comment: 27 page

IWIN: the Isfjorden Weather Information Network

In an effort led by the University Centre in Svalbard (UNIS), with support from the Norwegian Meteorological Institute (MET Norway), the Isfjorden Weather Information Network (IWIN) is under development in the Isfjorden region in central Svalbard. The network substantially expands upon the relatively sparse existing operational network of weather stations and consists of compact and cost-efficient all-in-one weather stations permanently installed at lighthouses around Isfjorden and on board small tourist cruise ships trafficking the fjord from spring to autumn. All data from the network until June 2023, as presented in this paper, can be found at https://doi.org/10.5281/zenodo.8137588 (Frank et al., 2023b). New data become freely available in near-real time via MET Norway's data portals (https://doi.org/10.21343/ebrw-w846, Frank et al., 2023a). The IWIN data are highly valuable for scientific purposes such as atmospheric boundary layer research, the validation and development of numerical weather prediction models, and assimilation in these, as well as the planning and safe conduction of outdoor activities in the region.</p

A strong pair correlation bound implies the CLT for Sinai Billiards

For Dynamical Systems, a strong bound on multiple correlations implies the Central Limit Theorem (CLT) [ChMa]. In Chernov's paper [Ch2], such a bound is derived for dynamically Holder continuous observables of dispersing Billiards. Here we weaken the regularity assumption and subsequently show that the bound on multiple correlations follows directly from the bound on pair correlations. Thus, a strong bound on pair correlations alone implies the CLT, for a wider class of observables. The result is extended to Anosov diffeomorphisms in any dimension.Comment: 13 page