Cell Cycle–Specified Fluctuation of Nucleosome Occupancy at Gene Promoters

The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G(2)/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence

Template-induced structuring and tunable polymorphism of three-dimensionally ordered mesoporous (3DOm) metal oxides

Convectively assembled colloidal crystal templates, composed of size-tunable (ca. 15–50 nm) silica (SiO2) nanoparticles, enable versatile sacrificial templating of three-dimensionally ordered mesoporous (3DOm) metal oxides (MOx) at both mesoscopic and microscopic size scales. Specifically, we show for titania (TiO2) and zirconia (ZrO2) how this approach not only enables the engineering of the mesopore size, pore volume, and surface area but can also be leveraged to tune the crystallite polymorphism of the resulting 3DOm metal oxides. Template-mediated volumetric (i.e., interstitial) effects and interfacial factors are shown to preserve the metastable crystalline polymorphs of each corresponding 3DOm oxide (i.e., anatase TiO2 (A-TiO2) and tetragonal ZrO2 (t-ZrO2)) during high-temperature calcination. Mechanistic investigations suggest that this polymorph stabilization is derived from the combined effects of the template–replica (MOx/SiO2) interface and simultaneous interstitial confinement that limit the degree of coarsening during high-temperature calcination of the template–replica composite. The result is the identification of a facile yet versatile templating strategy for realizing 3DOm oxides with (i) surface areas that are more than an order of magnitude larger than untemplated control samples, (ii) pore diameters and volumes that can be tuned across a continuum of size scales, and (iii) selectable polymorphism

UAS Surveillance Criticality

The integration of unmanned aircraft systems (UAS) into the national airspace system (NAS) poses considerable challenges. Maintaining human safety is perhaps chief among these challenges as UAS remote pilots will need to interact with other UAS, piloted aircraft, and other conditions associated with flight. A research team of 6 leading UAS research universities was formed to respond to a set of surveillance criticality research questions. Five analysis tools were selected following a literature review to evaluate airborne surveillance technology performance. The analysis tools included: Fault Trees, Monte Carlo Simulations, Hazard Analysis, Design of Experiments (DOE), and Human-in-the-Loop Simulations. The Surveillance Criticality research team used results from these analyses to address three primary research questions and provide recommendations for UAS detect-and-avoid mitigation and areas for further research

Integrated Blade Inspection System (IBIS) Upgrade Study

The purpose of this design study was to identify ways to improve the Integrated Blade Inspection System. The Air Force requires inspection of jet engine compressor and turbine blades to locate defects and prevent engine failure. The current inspection process uses fluorescent penetrant as an aid to identify cracked blades. A systems engineering design process was applied to evaluate the current inspection techniques and to develop alternative methods to satisfy the Air Force requirements. Three different inspection systems were developed and compared to the current process: manual, semi-automated, and fully automated inspection. This study made several noteworthy contributions: development of classification software to validate the neural network approach for accurate blade classification, demonstration of potential advantages of charge-coupled device cameras for data gathering, quantification of the cost of incorrectly classifying jet engine blades, examination of the value of a statistical quality control plan for the inspection process, and identification of a method using multiple images to extract additional features from cracks. The study demonstrates that the fully automated system could dramatically outperform the manual inspection process by improving the consistency of the inspection process and raising the quality of the blades returned to service

z~2: An Epoch of Disk Assembly

We explore the evolution of the internal gas kinematics of star-forming galaxies from the peak of cosmic star-formation at $z\sim2$ to today. Measurements of galaxy rotation velocity $V_{rot}$, which quantify ordered motions, and gas velocity dispersion $\sigma_g$, which quantify disordered motions, are adopted from the DEEP2 and SIGMA surveys. This sample covers a continuous baseline in redshift from $z=2.5$ to $z=0.1$, spanning 10 Gyrs. At low redshift, nearly all sufficiently massive star-forming galaxies are rotationally supported ($V_{rot}>\sigma_g$). By $z=2$, the percentage of galaxies with rotational support has declined to 50$\%$ at low stellar mass ($10^{9}-10^{10}\,M_{\odot}$) and 70$\%$ at high stellar mass ($10^{10}-10^{11}M_{\odot}$). For $V_{rot}\,>\,3\,\sigma_g$, the percentage drops below 35$\%$ for all masses. From $z\,=\,2$ to now, galaxies exhibit remarkably smooth kinematic evolution on average. All galaxies tend towards rotational support with time, and it is reached earlier in higher mass systems. This is mostly due to an average decline in $\sigma_g$ by a factor of 3 since a redshift of 2, which is independent of mass. Over the same time period, $V_{rot}$ increases by a factor of 1.5 for low mass systems, but does not evolve for high mass systems. These trends in $V_{rot}$ and $\sigma_g$ with time are at a fixed stellar mass and should not be interpreted as evolutionary tracks for galaxy populations. When galaxy populations are linked in time with abundance matching, not only does $\sigma_g$ decline with time as before, but $V_{rot}$ strongly increases with time for all galaxy masses. This enhances the evolution in $V_{rot}/\sigma_g$. These results indicate that $z\,=\,2$ is a period of disk assembly, during which the strong rotational support present in today's massive disk galaxies is only just beginning to emerge.Comment: 12 pages, 8 figures, submitted to Ap

The Magnetohydrodynamics of Shock-Cloud Interaction in Three Dimensions

The magnetohydrodynamic evolution of a dense spherical cloud as it interacts with a strong planar shock is studied, as a model for shock interactions with density inhomogeneities in the interstellar medium. The cloud is assumed to be small enough that radiative cooling, thermal conduction, and self-gravity can be ignored. A variety of initial orientations (including parallel, perpendicular, and oblique to the incident shock normal) and strengths for the magnetic field are investigated. During the early stages of the interaction (less than twice the time taken for the transmitted shock to cross the interior of the cloud) the structure and dynamics of the shocked cloud is fairly insensitive to the magnetic field strength and orientation. However, at late times strong fields substantially alter the dynamics of the cloud, suppressing fragmentation and mixing by stabilizing the interface at the cloud surface. Even weak magnetic fields can drastically alter the evolution of the cloud compared to the hydrodynamic case. Weak fields of different geometries result in different distributions and amplifications of the magnetic energy density, which may affect the thermal and non-thermal x-ray emission expected from shocked clouds associated with, for example, supernovae remnants.Comment: Accepted for publication in Astrophysical Journal; a higher resolution file can be found at http://www.astro.princeton.edu/~msshin/science/shock_cloud.pdf.g

Finding the Needles in the Haystacks: High-Fidelity Models of the Modern and Archean Solar System for Simulating Exoplanet Observations

We present two state-of-the-art models of the solar system, one corresponding to the present day and one to the Archean Eon 3.5 billion years ago. Each model contains spatial and spectral information for the star, the planets, and the interplanetary dust, extending to 50 AU from the sun and covering the wavelength range 0.3 to 2.5 micron. In addition, we created a spectral image cube representative of the astronomical backgrounds that will be seen behind deep observations of extrasolar planetary systems, including galaxies and Milky Way stars. These models are intended as inputs to high-fidelity simulations of direct observations of exoplanetary systems using telescopes equipped with high-contrast capability. They will help improve the realism of observation and instrument parameters that are required inputs to statistical observatory yield calculations, as well as guide development of post-processing algorithms for telescopes capable of directly imaging Earth-like planets.Comment: Accepted for publication in PAS

Modeling Mid-infrared Diagnostics of Obscured Quasars and Starbursts

We analyze the link between active galactic nuclei (AGNs) and mid-infrared flux using dust radiative transfer calculations of starbursts realized in hydrodynamical simulations. Focusing on the effects of galaxy dust, we evaluate diagnostics commonly used to disentangle AGN and star formation in ultraluminous infrared galaxies (ULIRGs). We examine these quantities as a function of time, viewing angle, dust model, AGN spectrum, and AGN strength in merger simulations representing two possible extremes of the ULIRG population: one is a typical gas-rich merger at z ~ 0, and the other is characteristic of extremely obscured starbursts at z ~ 2-4. This highly obscured burst begins star-formation-dominated with significant polycyclic aromatic hydrocarbon (PAH) emission, and ends with a ~10^9 yr period of red near-IR colors. At coalescence, when the AGN is most luminous, dust obscures the near-infrared AGN signature, reduces the relative emission from PAHs, and enhances the 9.7 μm absorption by silicate grains. Although generally consistent with previous interpretations, our results imply none of these indicators can unambiguously estimate the AGN luminosity fraction in all cases. Motivated by the simulations, we show that a combination of the extinction feature at 9.7 μm, the PAH strength, and a near-infrared slope can simultaneously constrain the AGN fraction and dust grain distribution for a wide range of obscuration. We find that this indicator, accessible to the James Webb Space Telescope, may estimate the AGN power as tightly as the hard X-ray flux alone, thereby providing a valuable future cross-check and constraint for large samples of distant ULIRGs

Interfacial stabilization of metastable TiO2 films

This work demonstrates a phenomenon that preserves the traditionally metastable anatase crystal structure of thin titania (TiO2) films along a two-dimensional oxide interface at temperatures well in excess of those that normally trigger a full polymorphic transformation to rutile in higher dimensionality crystalline powders. Whereas atomic surface mobility appears to dominate polymorph transformation processes within bulk TiO2 powders, a simple reduction in dimensionality to a two-dimensional TiO2 film (ca. 50–200 nm thick), supported upon a substrate, leads to a remarkable resistance to the calcination-induced anatase-to-rutile transformation. This stabilization does not appear to be specifically reliant on substrate character given its persistence for TiO2 films prepared on amorphous silica (SiO2) as well as crystalline TiO2 substrates. Instead, interface-mediated coordination of the TiO2 film with the substrate, and the inherent confinement of crystallites in two dimensions, is believed to resist polymorph transformation by mitigation of the atomic surface mobility. Only when temperatures (i.e., >800 °C) that are conducive to bulk atomic mobilization are reached does reconstructive grain growth convert the film into the thermodynamically stable rutile crystal structure