Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions
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59 BASIC BIOLOGICAL SCIENCES↗
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Gamma ray interaction processes
Gamma ray detection in the energy region above 1 keV involves measurements of the energy exchange or energy loss between the gamma ray and the mass of the detector. In most cases of interest, it is the kinetic energy imparted to charged particles by the gamma ray which is lost in the detector and measured in order to obtain spectral knowledge between the incident gamma ray photon and the direction of the secondary particles contains important energy information. The interaction gamma ray removal processes in matter are considered. This interaction removal process is characterized by the fact that each gamma ray is removed individually from the incident beam. The number of photons removed in this manner is proportional to the thickness of matter traversed.
Source record↗
Testing shell-model interactions at high excitation energy and low spin: Nuclear resonance fluorescence in Ge 74
With their complex low-spin structure, the germanium isotopes have accrued a large number of experimental data which challenge nuclear models. The structure of the 74 Ge isotope is investigated here with nuclear resonance fluorescence as part of an extensive campaign of experimental tests of the shell model in the germanium isotopic chain using a number of complementary techniques. Levels were excited with 3.10 – 5.44 MeV photon beams provided by the High Intensity Gamma-Ray Source at TUNL. Many new levels were identified and their spins, parities, branching ratios, and associated scattering cross section values were determined. Large-scale shell-model calculations, which include jj44b and JUN45 effective interactions developed to describe nuclei in this mass region, predict the new data satisfactorily. Herein this study extends the validation of these two interactions, which are candidates for computation of matrix elements to be used in the interpretation of neutrinoless double-β decay experiments in 76 Ge, into the low-spin, high excitation energy domain.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
LxCxD motif of the APC/C coactivator subunit FZR1 is critical for interaction with the retinoblastoma protein
Highlights: • Several oncogenic viral proteins bind to tumor suppressor pRB via LxCxE motif. • LxCxE present in many cellular proteins that interact with pRB. • APC/C interacts with pRB via this motif in its FZR1 subunit. • FZR1 LxCxE-like LxCxD critical for FZR1-pRB direct binding and SKP2 ubiquitylation. • Mutation of FZR1 LxCxD alters cell cycle. Retinoblastoma protein (pRB) regulates cell cycle by utilizing different regions of its pocket domain for interacting with E2F family of transcription factors and with cellular and viral proteins containing an LxCxE motif. An LxCxE-like motif, LxCxD, is present in FZR1, an adaptor protein of the multi-subunit E3 ligase complex anaphase-promoting complex/cyclosome (APC/C). The APC/C{sup FZR1} complex regulates the timely degradation of multiple cell cycle proteins for mitotic exit and maintains G1 state. We report that FZR1 interacts with pRB via its LxCxD motif. By using point mutations, we found that the cysteine residue in the FZR1 LxCxD motif is critical for direct interaction with pRb. The direct binding of the LxCxD motif of FZR1 to the pRB LxCxE binding pocket is confirmed by using human papillomavirus protein E7 as a competitor, both in vitro and in vivo. While mutation of the cysteine residue significantly disrupts FZR1 interaction with pRB, this motif does not affect FZR1 and core APC/C association. Expression of the FZR1 point mutant results in accumulation of S-phase kinase-associated protein 2 (SKP2) and Polo-like kinase 1 (PLK1), while p27{sup Kip1} and p21{sup Cip1} proteins are downregulated, indicating a G1 cell cycle defect. Consistently, cells containing point mutant FZR1 enter the S phase prematurely. Together our results suggest that the LxCxD motif of FZR1 is a critical determinant for the interaction between FZR1 and pRB and is important for G1 restriction.
60 APPLIED LIFE SCIENCES↗
Long wavelength gradient drift instability in Hall plasma devices. II. Applications
Hall plasma devices with electron E × B drift are subject to a class of long wavelength instabilities driven by the electron current, gradients of plasma density, temperature, and magnetic field. In the first companion paper [Frias et al., Phys. Plasmas 19, 072112 (2012)], the theory of these modes was revisited. In this paper, we apply analytical theory to show that modern Hall thrusters exhibit azimuthal and axial oscillations in the frequency spectrum from tens KHz to few MHz, often observed in experiments. The azimuthal phase velocity of these modes is typically one order of magnitude lower than the E × B drift velocity. The growth rate of these modes scales inversely with the square root of the ion mass, ∼1/√(m){sub i}. It is shown that several different thruster configurations share the same common feature: the gradient drift instabilities are localized in two separate regions, near the anode and in the plume region, and absent in the acceleration region. Our analytical results show complex interaction of plasma and magnetic field gradients and the E × B drift flow as the sources of the instability. The special role of plasma density gradient is revealed and it is shown that the previous theory is not applicable in the region where the ion flux density is not uniform. This is particularly important for near anode region due to ionization and in the plume region due to diverging ion flux.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c
Redox-dependent changes in the structure and dynamics of human cytochrome c (Cyt c) were investigated by solution NMR. We found significant structural changes in several regions, including residues 23–28 (loop 3), which were further corroborated by chemical shift differences between the reduced and oxidized states of Cyt c. These differences are essential for discriminating redox states in Cyt c by cytochrome c oxidase (CcO) during electron transfer reactions. Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments identified that the region around His33 undergoes conformational exchanges on the μs-ms timescale, indicating significant redox-dependent structural changes. Because His33 is not part of the interaction site for CcO, our data suggest that the dynamic properties of the region, which is far from the interaction site for CcO, contribute to conformational changes during electron transfer to CcO. - Highlights: • Solution structure and dynamics analysis for human Cyt c by NMR. • Structural changes responsible for the discrimination of the redox state in Cyt c. • Conformational exchange in the region outside of the interaction site for CcO. • Less flexibility and rigid structure of the interaction site on Cyt c for CcO.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Numerical modelling of evaporation in a ceramic layer in the tape casting process
Evaporation of water from a ceramic layer is a key phenomenon in the drying process for the manufacturing of tape cast ceramics. This process contains mass, momentum and energy exchange between the porous medium and the free–flow region. In order to analyze such interaction processes, a Representative Elementary Volume (REV)–scale model concept is presented for coupling non–isothermal multi–phase compositional porous–media flow and single–phase compositional laminar free–flow. The preliminary results show the typical expected evaporation behaviour from a porous medium initially saturated with water, and its transport to the free–flow region according to the existent results from the literature.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Improving the Top Quark Forward-Backward Asymmetry Measurement at the LHC
At the LHC, top quark pairs are dominantly produced from gluons, making it difficult to measure the top quark forward-backward asymmetry. To improve the asymmetry measurement, we study variables that can distinguish between top quarks produced from quarks and those from gluons: the invariant mass of the top pair, the rapidity of the top-antitop system in the lab frame, the rapidity of the top quark in the top-antitop rest frame, the top quark polarization and the top-antitop spin correlation. We combine all the variables in a likelihood discriminant method to separate quark-initiated events from gluon-initiated events. We apply our method on models including G-prime's and W-prime's motivated by the recent observation of a large top quark forward-backward asymmetry at the Tevatron. We have found that the significance of the asymmetry measurement can be improved by 10% to 30%. At the same time, the central values of the asymmetry increase by 40% to 100%. We have also analytically derived the best spin quantization axes for studying top quark polarization as well as spin-correlation for the new physics models.
43 PARTICLE ACCELERATORS↗
On reflecting boundary behind the Earth's orbit at propagation of fast particles from solar flares
The flares of solar cosmic rays (SCR) associated with the presence of shocks in interplanetary magnetic field and with their propagation at significant heliocentric distances were always of great interest. Some events and problems concerning the peculiarities of propagation of flare CR in the interplanetary medium are considered. The distinguishing feature of such events is the presence of shock front behind the Earth's orbit having formed either directly in the process of shock generation on the Sun or at large heliocentric distances as a result of the interaction of fast and slow quasistationary recurrent solar wind (SW) streams. Based on the experimental material it is shown that the significant nonlinear disturbances in IMF behind the Earth's orbit can yield the occurrence of the additional SCR flux from shock front region as a result of the interaction of flare flux with shock and a partial reflection from it.
Nishkovskikh, A. S.↗
Cloud Masking and Surface Temperature Distribution in the Polar Regions Using AVHRR and other Satellite Data
Surface temperature is one of the key variables associated with weather and climate. Accurate measurements of surface air temperatures are routinely made in meteorological stations around the world. Also, satellite data have been used to produce synoptic global temperature distributions. However, not much attention has been paid on temperature distributions in the polar regions. In the polar regions, the number of stations is very sparse. Because of adverse weather conditions and general inaccessibility, surface field measurements are also limited. Furthermore, accurate retrievals from satellite data in the region have been difficult to make because of persistent cloudiness and ambiguities in the discrimination of clouds from snow or ice. Surface temperature observations are required in the polar regions for air-sea-ice interaction studies, especially in the calculation of heat, salinity, and humidity fluxes. They are also useful in identifying areas of melt or meltponding within the sea ice pack and the ice sheets and in the calculation of emissivities of these surfaces. Moreover, the polar regions are unique in that they are the sites of temperature extremes, the location of which is difficult to identify without a global monitoring system. Furthermore, the regions may provide an early signal to a potential climate change because such signal is expected to be amplified in the region due to feedback effects. In cloud free areas, the thermal channels from infrared systems provide surface temperatures at relatively good accuracies. Previous capabilities include the use of the Temperature Humidity Infrared Radiometer (THIR) onboard the Nimbus-7 satellite which was launched in 1978. Current capabilities include the use of the Advance Very High Resolution Radiometer (AVHRR) aboard NOAA satellites. Together, these two systems cover a span of 16 years of thermal infrared data. Techniques for retrieving surface temperatures with these sensors in the polar regions have been developed. Errors have been estimated to range from 1K to 5K mainly due to cloud masking problems. With many additional channels available, it is expected that the EOS-Moderate Resolution Imaging Spectroradiometer (MODIS) will provide an improved characterization of clouds and a good discrimination of clouds from snow or ice surfaces.
Comiso, Joey C.↗
Recent observations and analyses of heliospheric 2-3 kHz radio emissions
Since the discovery of the 2-3 kHz heliospheric radio emissions in the Voyager data over twelve years ago, there have been two major events, the first in 1983-84 and the second in 1992-93, as well as several minor events. Strong evidence now exists that these radio emissions are generated by interactions that take place in the outer regions of the heliosphere, most likely in response to strong interplanetary shocks and associated disturbances propagating outward from the Sun. Just where these interactions take place is still a subject of controversy. The three main possibilities are at or near the termination shock, between the termination shock and the heliopause and at or near the heliopause. In this paper we will review the present state of knowledge concerning the 2-3 kHz radio emissions, including the most recent data from Voyagers 1 and 2. These observations will then be compared to models that have been proposed to explain the origin of the radio emissions. Depending on the model, various estimates can be made concerning the plasma densities in the region where the radio emission is produced, and the distance to the source. The constraints provided by these models on the size and structure of the heliosphere are discussed.
Gurnett, D. A.↗
Signatures of self-interacting dark matter on cluster density profile and subhalo distributions
Non-gravitational interactions between dark matter particles with strong scattering, but relatively small annihilation and dissipation, has been proposed to match various observables on cluster and group scales. In this paper, we present the results from large cosmological simulations which include the effects of different self-interaction scenarios. In particular we explore a model with the differential cross section that can depend on both the relative velocity of the interacting particles and the angle of scattering. We focus on how quantities, such as the stacked density profiles, subhalo counts and the splashback radius change as a function of different forms of self-interaction. We find that self-interactions not only affect the central region of the cluster, the effect well known from previous studies, but also significantly alter the distribution of subhalos and the density of particles out to the splashback radius. Therefore, our results suggest that current weak lensing data can already put constraints on the self-interaction cross-section that are only slightly weaker than the Bullet Cluster constraints (σ/m ≲ 2 cm 2 /g), and future lensing surveys should be able to tighten them even further making halo profiles on cluster scales a competitive probe for DM physics.
79 ASTRONOMY AND ASTROPHYSICS↗
2p2h or not 2p2h?
This paper summarizes the discussion about the role of two-particle-two-hole (2p2h) excitations in neutrino-nucleus interactions in the few-GeV region, held at NuInt11.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Information-Theoretic Exploration of Multivariate Time-Varying Image Databases
Modern scientific simulations produce very large datasets, making interactive exploration of such data computationally prohibitive. An increasingly common data reduction technique is to store visualizations and other data extracts in a database. The Cinema project is one such approach, storing visualizations in an image database for post hoc exploration and interactive image-based analysis. This work focuses on developing efficient algorithms that can quantify various types of multivariate dependencies existing within multi-variable datasets. It applies specific mutual information measures for the quantification of salient regions from multivariate image data. Here, using such information measures, the opacity of the images is modulated so that the salient regions are automatically highlighted and the domain scientists can interactively explore the most relevant regions for scientific discovery.
97 MATHEMATICS AND COMPUTING↗
Structure-function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2
Abstract not provided
Chen, Shoudeng↗
Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography
Total chemical synthesis was used to prepare the mirror image (D-protein) form of the angiogenic protein vascular endothelial growth factor (VEGF-A). Phage display against D-VEGF-A was used to screen designed libraries based on a unique small protein scaffold in order to identify a high affinity ligand. Chemically synthesized D- and L- forms of the protein ligand showed reciprocal chiral specificity in surface plasmon resonance binding experiments: The L-protein ligand bound only to D-VEGF-A, whereas the D-protein ligand bound only to L-VEGF-A. The D-protein ligand, but not the L-protein ligand, inhibited the binding of natural VEGF{sub 165} to the VEGFR1 receptor. Racemic protein crystallography was used to determine the high resolution X-ray structure of the heterochiral complex consisting of {l_brace}D-protein antagonist + L-protein form of VEGF-A{r_brace}. Crystallization of a racemic mixture of these synthetic proteins in appropriate stoichiometry gave a racemic protein complex of more than 73 kDa containing six synthetic protein molecules. The structure of the complex was determined to a resolution of 1.6 {angstrom}. Detailed analysis of the interaction between the D-protein antagonist and the VEGF-A protein molecule showed that the binding interface comprised a contact surface area of approximately 800 {angstrom}{sup 2} in accord with our design objectives, and that the D-protein antagonist binds to the same region of VEGF-A that interacts with VEGFR1-domain 2.
59 BASIC BIOLOGICAL SCIENCES↗
Ice Nucleating Particle Connections to Regional Argentinian Land Surface Emissions and Weather During the Cloud, Aerosol, and Complex Terrain Interactions Experiment
Abstract Here, we present a multi‐season study of ice‐nucleating particles (INPs) active via the immersion freezing mechanism, which took place in north‐central Argentina, a worldwide hotspot for mesoscale convective storms. INPs were measured untreated, after heating to 95°C, and after hydrogen peroxide digestion. No seasonal cycle of INP concentrations was observed. Heat labile INPs, which we define as “biological” herein, dominated the population active at −5 to −20°C, while non‐heat‐labile organic INPs (decomposed by peroxide) dominated at lower temperatures, from −20 to −28°C. Inorganic INPs (remaining after peroxide digestion), were minor contributors to the overall INP activity. Biological INP concentration active around −12°C peaked during rain events and under high relative humidity, reflecting emission mechanisms independent of the background aerosol concentration. The ratio of non‐heat‐labile organic and inorganic INPs was generally constant, suggesting they originated from the same source, presumably from regional arable topsoil based on air mass histories. Single particle mass spectrometry showed that soil particles aerosolized from a regionally common agricultural topsoil contained known mineral INP sources (K‐feldspar and illite) as well as a significant organic component. The INP activity observed in this study correlates well with agricultural soil INP activities from this and other regions of the world, suggesting that the observed INP spectra might be typical of many arable landscapes. These results demonstrate the strong influence of regional continental landscapes, emitting INPs of types that are not yet well represented in global models.
54 ENVIRONMENTAL SCIENCES↗
GiBUU and Neutrino-Nucleus scattering
The Giessen BUU transport approach applied to electroweak interactions on nuclei in the few-GeV region is presented. After describing the model ingredients (elementary cross sections, medium effects and final state interactions), the impact of nuclear effects on the observables is discussed. We emphasize the interconnection of quasielastic and pion production processes, which receive a unified treatment, and its relevance for present neutrino experiments.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
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