Genomic data analysis using DNA structure: an analysis of conserved nongenic sequences and ultraconserved elements

Recent comparative studies of the human and mouse genomes have revealed sets of conserved nongenic sequences (CNGs) and sets of ultraconserved elements (UCEs). Both sets of sequences, which exhibit extremely high levels of conservation, extend over hundreds of bases and have no known function. Since there is no detectable sequence homology between paralogous CNGs or UCEs in either of the species, an alignment-free technique is needed for their analysis. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers, including information on stability, the minimum energy conformation, and flexibility. We have used Fourier techniques to analyze the UCEs and CNGs in terms of their octamer structural properties, to reveal structural correlations which may indicate possible functions for some of these sequences.     

Graphitic encapsulation of catalyst particles in carbon nanotube production

A new model is proposed for the encapsulation of catalyst metal particles by graphite layers that are obtained, for example, in low-temperature chemical vapor deposition production of carbon nanotubes (CNTs). In this model graphite layers are primarily formed from the dissolved carbon atoms in the metal-carbide particle when the particle cools. This mechanism is in good agreement with molecular dynamics simulations (which show that precipitated carbon atoms preferentially form graphite sheets instead of CNTs at low temperatures) and experimental results (e.g., encapsulated metal particles are found in low-temperature zones and CNTs in high-temperature regions of production apparatus, very small catalyst particles are generally not encapsulated, and the ratio of the number of graphitic layers to the diameter of the catalyst particle is typically 0.25 nm(-1)).     

Microbial dynamics in oil-impacted prairie soil

A remote site in the Tallgrass Prairie Preserve (Osage County, OK) was contaminated with crude oil by a pipeline break in 1992. In 1996, the contaminated soil was bioremediated by blending with uncontaminated soil, prairie hay, buffalo manure, and commercial fertilizers, and spreading in a shallow layer over uncontaminated soil to create a landfarm. The landfarm was monitored for two years for aerobic and anaerobic bacteria, soil gases indicative of microbial activity, and for changes in the concentration of total petroleum hydrocarbons (TPH). Levels of hydrocarbon degraders and soil gas indicators of aerobic degradation were stimulated in the landfarm during the first warm season relative to uncontaminated prairie soil. However, these same indicators were less conclusive during the second warm season, indicating depletion of the more easily degradable hydrocarbons, although the landfarm still contained 6,800 mg/kg TPH on the average at the beginning of the second warm season. Methane formation and methanogen counts were clearly stimulated in the first warm season relative to uncontaminated prairie soil, in dicating that methanogenesis plays an important role in the mineralization of hydrocarbons even in these shallow soils.     

Plasmalemmal Vesicle Associated Protein-1 (PV-1) is a marker of blood-brain barrier disruption in rodent models

Background  

Plasmalemmal vesicle associated protein-1 (PV-1) is selectively expressed in human brain microvascular endothelial cells derived from clinical specimens of primary and secondary malignant brain tumors, cerebral ischemia, and other central nervous system (CNS) diseases associated with blood-brain barrier breakdown. In this study, we characterize the murine CNS expression pattern of PV-1 to determine whether localized PV-1 induction is conserved across species and disease state.     

Discrete mass conservation for porous media saturated flow

Global and local mass conservation for velocity fields associated with saturated porous media flow have long been recognized as integral components of any numerical scheme attempting to simulate these flows. In this work, we study finite element discretizations for saturated porous media flow that use Taylor–Hood (TH) and Scott–Vogelius (SV) finite elements. The governing equations are modified to include a stabilization term when using the TH elements, and we provide a theoretical result that shows convergence (with respect to the stabilization parameter) to pointwise mass‐conservative solutions. We also provide results using the SV approximation pair. These elements are pointwise divergence free, leading to optimal convergence rates and numerical solutions. We give numerical results to verify our theory and a comparison with standard mixed methods for saturated flow problems. © 2013 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 30: 625–640, 2014     

Probing Rapidly‐Ionizing Super‐Atom Molecular Orbitals in C60: A Computational and Femtosecond Photoelectron Spectroscopy Study

Super‐atom molecular orbitals (SAMOs) are diffuse hydrogen‐like orbitals defined by the shallow potential at the centre of hollow molecules such as fullerenes. The SAMO excited states differ from the Rydberg states by the significant electronic density present inside the carbon cage. We provide a detailed computational study of SAMO and Rydberg states and an experimental characterization of SAMO excited electronic states for gas‐phase C₆₀ molecules by photoelectron spectroscopy. A large band of 500 excited states was computed using time‐dependent density functional theory. We show that due to their diffuse character, the photoionization widths of the SAMO and Rydberg states are orders of magnitude larger than those of the isoenergetic non‐SAMO excited states. Moreover, in the range of kinetic energies experimentally measured, only the SAMO states photoionize significantly on the timescale of the femtosecond laser experiments. Single photon ionization of the SAMO states dominates the photoelectron spectrum for relatively low laser intensities. The computed photoelectron spectra and photoelectron angular distributions are in good agreement with the experimental results.     

Effect of Silk Protein Processing on Drug Delivery from Silk Films

Sericin removal from the core fibroin protein of silkworm silk is a critical first step in the use of silk for biomaterial‐related applications, but degumming can affect silk biomaterial properties, including molecular weight, viscosity, diffusivity and degradation behavior. Increasing the degumming time (10, 30, 60, and 90 min) decreases the average molecular weight of silk protein in solution, silk solution viscosity, and silk film glass‐transition temperature, and increases the rate of degradation of a silk film by protease. Model compounds spanning a range of physical‐chemical properties generally show an inverse relationship between degumming time and release rate through a varied degumming time silk coating. Degumming provides a useful control point to manipulate silk's material properties.