Transcription start site scanning and the requirement for ATP during transcription initiation by RNA polymerase II

Saccharomyces cerevisiae RNA polymerase (Pol) II locates transcription start sites (TSS) at TATA-containing promoters by scanning sequences downstream from the site of preinitiation complex formation, a process that involves the translocation of downstream promoter DNA toward Pol II. To investigate a potential role of yeast Pol II transcription in TSS scanning, HIS4 promoter derivatives were generated that limited transcripts in the 30-bp scanned region to two nucleotides in length. Although we found that TSS scanning does not require RNA synthesis, our results revealed that transcription in the purified yeast basal system is largely ATP-independent despite a requirement for the TFIIH DNA translocase subunit Ssl2. This result is rationalized by our finding that, although they are poorer substrates, UTP and GTP can also be utilized by Ssl2. ATPγS is a strong inhibitor of rNTP-fueled translocation, and high concentrations of ATPγS make transcription completely dependent on added dATP. Limiting Pol II function with low ATP concentrations shifted the TSS position downstream. Combined with prior work, our results show that Pol II transcription plays an important role in TSS selection but is not required for the scanning reaction

First principles analysis of lattice dynamics for Fe-based superconductors and entropically-stabilized phases

Modern ab initio calculations are becoming an essential, complementary tool to inelastic x-ray scattering studies, where x-rays are scattered inelastically to resolve meV phonons. Calculations of the inelastic structure factor for any value of Q assist in both planning the experiment and analyzing the results. Moreover, differences between the measured data and theoretical calculations help identify important new physics driving the properties of novel correlated systems. We have used such calculations to better and more efficiently measure the phonon dispersion and elastic constants of several iron pnictide superconductors. This dissertation describes calculations and measurements at room temperature in the tetragonal phase of CaFe2As2 and LaFeAsO. In both cases, spin-polarized calculations imposing the antiferromagnetic order present in the low-temperature orthorhombic phase dramatically improves the agreement between theory and experiment. This is discussed in terms of the strong antiferromagnetic correlations that are known to persist in the tetragonal phase. In addition, we discuss a relatively new approach called self-consistent ab initio lattice dynamics (SCAILD), which goes beyond the harmonic approximation to include phonon-phonon interactions and produce a temperature-dependent phonon dispersion. We used this technique to study the HCP to BCC transition in beryllium

A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex.

To directly map the position of promoter DNA within the RNA polymerase II (Pol II) transcription preinitiation complex (PIC), FeBABE was tethered to specific sites within the HIS4 promoter and used to map exposed surfaces of Pol II and the general transcription factors in proximity to DNA. Our results distinguish between previously proposed models for PIC structure and demonstrate that downstream promoter DNA is positioned over the central cleft of Pol II, with DNA upstream of TATA extending toward the Pol II subunit Rpb3. Also mapped were segments of TFIIB, TFIIE, TFIIF and TFIIH in proximity to promoter DNA. DNA downstream of the transcription bubble maps to a path between the two helicase subdomains of the TFIIH subunit Rad25 (also called XPB). Together, our results show how the general factors and Pol II converge on promoter DNA within the PIC

Low Cost Large Core Vehicle Structures Assessment

Boeing Information, Space, and Defense Systems executed a Low Cost Large Core Vehicle Structures Assessment (LCLCVSA) under contract to NASA Marshall Space Flight Center (MSFC) between November 1997 and March 1998. NASA is interested in a low-cost launch vehicle, code named Magnum, to place heavy payloads into low earth orbit for missions such as a manned mission to Mars, a Next Generation Space Telescope, a lunar-based telescope, the Air Force's proposed space based laser, and large commercial satellites. In this study, structural concepts with the potential to reduce fabrication costs were evaluated in application to the Magnum Launch Vehicle (MLV) and the Liquid Fly Back Booster (LFBB) shuttle upgrade program. Seventeen concepts were qualitatively evaluated to select four concepts for more in-depth study. The four structural concepts selected were: an aluminum-lithium monocoque structure, an aluminum-lithium machined isogrid structure, a unitized composite sandwich structure, and a unitized composite grid structure. These were compared against a baseline concept based on the Space Shuttle External Tank (ET) construction. It was found that unitized composite structures offer significant cost and weight benefits to MLV structures. The limited study of application to LFBB structures indicated lower, but still significant benefits. Technology and facilities development roadmaps to prepare the approaches studied for application to MLV and LFBB were constructed. It was found that the cost and schedule to develop these approaches were in line with both MLV and LFBB development schedules. Current Government and Boeing programs which address elements of the development of the technologies identified are underway. It is recommended that NASA devote resources in a timely fashion to address the specific elements related to MLV and LFBB structures

Complements and Meat Demand in the U.S.

In this study we estimated the price elasticities among meats, vegetables, grains, and potatoes and the impact that different levels of income have on the demand for these commodities. The 2005 Nielsen retail home scan data were used to construct a censored demand system of 14 equations. Results revealed that the uncompensated cross-price elasticities for both low and high-incomes suggest both substitution and complement relationships, while the compensated price elasticities are dominated primarily by substitution relationships. Our findings also revealed that expenditure elasticities among both low and high-income households differ for most commodities.censored dependent variables, meats, poultry, fish, vegetables, sample selection model, two-step estimation, Demand and Price Analysis, Livestock Production/Industries, C25, D12, Q11,

Rhesus Monkey Rhadinovirus Uses Eph Family Receptors for Entry into B Cells and Endothelial Cells but Not Fibroblasts

Cellular Ephrin receptor tyrosine kinases (Ephrin receptors, Ephs) were found to interact efficiently with the gH/gL glycoprotein complex of the rhesus monkey rhadinovirus (RRV). Since EphA2 was recently identified as a receptor for the Kaposi's sarcoma-associated herpesvirus (KSHV) (Hahn et al., Nature Medicine 2012), we analyzed RRV and KSHV in parallel with respect to Eph-binding and Eph-dependent entry. Ten of the 14 Eph proteins, including both A- and B-type, interacted with RRV gH/gL. Two RRV strains with markedly different gH/gL sequences exhibited similar but slightly different binding patterns to Ephs. gH/gL of KSHV displayed high affinity towards EphA2 but substantially weaker binding to only a few other Ephs of the A-type. Productive entry of RRV 26-95 into B cells and into endothelial cells was essentially completely dependent upon Ephs since expression of a GFP reporter cassette from recombinant virus could be blocked to greater than 95% by soluble Eph decoys using these cells. In contrast, entry of RRV into fibroblasts and epithelial cells was independent of Ephs by these same criteria. Even high concentrations and mixtures of soluble Eph decoys were not able to reduce by any appreciable extent the number of fibroblasts and epithelial cells productively entered by RRV. Thus, RRV is similar to its close relative KSHV in the use of Eph family receptors for productive entry into B cells and endothelial cells. However, RRV uses a separate, distinct, Eph-independent pathway for productive entry into fibroblasts and epithelial cells. Whether KSHV also uses an Eph-independent pathway in some circumstances or to some extent remains to be determined