The Effects of Multiple Mutations in the Hydrophobic Core Upon the Stability of Staphylococcal Nuclease

Previous work in the laboratory of my research advisor, Dr. Wesley Stites, has investigated the core packing of the protein staphylococcal nuclease. The core of a protein is critical in determining a protein\u27s structure and stability. The hydrophobicity of the core has long been thought to be the principal driving force for folding, but recent work in the Stites lab has shown that optimization of van der Waals contacts and minimization of cavities, in our shorthand term, packing, is at least as energetically important. We are building upon this information in our attempt to better pack the protein core. If we can do this, we predict that the improvement in packing will make the protein more stable overall. This project takes a closer look at the thermodynamically unfavorable left-handed alpha helix region in the core of staphylococcal nuclease. It has already been shown that there are angle strains on some of the residue; that can be repaired by replacing the leucine at residue 38 with glycine. However, this created empty space within the core that greatly destabilized the protein. Our hypothesis was that by filling this space with larger amino acids at nearby locations, we would be able to correct this problem. Several mutations were made at residues 38, 39, and 125. The residues are all within close contact with each other and in the vicinity of the left-handed alpha helix. The following procedures were used: Kunkel DNA mutagenesis, transformation and preparation of M13 single stranded DNA, transfer of nuclease mutant gene from M13 to plasmid, Laemmli discontinuous protein SDS-Page gel, protein preparation and purification, and fluorometric titration. The hypothesis that relieving angle strain near the lefthanded alpha helix with a glycine, and then filling the space caused by that mutation with larger amino acids near it would increase the protein\u27s stability was confirmed. However, new packing problems were generated so most mutations resulted in an overall decrease in stability

The low-redshift intergalactic medium as seen in archival legacy Hubble/STIS and FUSE data

We present a comprehensive catalog of ultraviolet HST/STIS and FUSE absorbers in the low-redshift IGM at z<0.4. The catalog draws from the extensive literature on IGM absorption, and it reconciles discrepancies among previous catalogs through a critical evaluation of all reported absorption features in light of new HST/COS data. We report on 746 HI absorbers down to a rest-frame equivalent width of 12 milliAngstroms over a maximum redshift path length Deltaz=5.38. We also confirm 111 OVI absorbers, 29 CIV absorbers, and numerous absorption features due to other metal ions. We characterize the distribution of absorber line frequency as a function of column density as a power law, dN/dz \propto N^{-beta}, where beta=2.08+-0.12 for OVI and beta=1.68+-0.03 for HI. Utilizing a more sophisticated accounting technique than past work, the catalog accounts for ~43% of the baryons: 24+-2% in the photoionized Ly-alpha forest and 19+-2% in the WHIM as traced by OVI. We discuss the large systematic effects of various assumed metallicities and ionization states on these calculations, and we implement recent simulation results in our estimates.Comment: 18 pages, 9 figures, 2 machine readable tables; Submitted to The Astrophysical Journa

DISTRIBUTIONAL IMPACTS OF CAPPING ELIGIBILITY FOR COMMODITY PROGRAM PAYMENTS

Adjusted Gross Income, Commodity Payments, Eligibility, Means Test, Resource /Energy Economics and Policy, Q12, Q18,

An X-ray WHIM metal absorber from a Mpc-scale empty region of space

We report a detection of an absorption line at ~44.8 {\AA} in a > 500 ks Chandra HRC-S/LETG X-ray grating spectrum of the blazar H 2356-309. This line can be identified as intervening CV-K{\alpha} absorption, at z\approx0.112, produced by a warm (log T = 5.1 K) intergalactic absorber. The feature is significant at a 2.9{\sigma} level (accounting for the number of independent redshift trials). We estimate an equivalent hydrogen column density of log N_H=19.05 (Z/Zsun)^-1 cm^-2. Unlike other previously reported FUV/X-ray metal detections of warm-hot intergalactic medium (WHIM), this CV absorber lies in a region with locally low galaxy density, at ~2.2 Mpc from the closest galaxy at that redshift, and therefore is unlikely to be associated with an extended galactic halo. We instead tentatively identify this absorber with an intervening Warm-Hot Intergalactic Medium filament possibly permeating a large-scale, 30 Mpc extended, structure of galaxies whose redshift centroid, within a cylinder of 7.5 Mpc radius centered on the line of sight to H 2356-309, is marginally consistent (at a 1.8{\sigma} level) with the redshift of the absorber.Comment: ApJ accepted, 6 pages, 3 figure

Analyzing FSA Direct Loan Borrower Payback Histories: Predictors of Financial Improvement and Loan Servicing Actions

Classical and count data regression models are estimated to predict improvement in three key financial indicators—net worth, debt-to-asset ratio and current ratio—as well as the number of loan restructurings and delinquencies. Data consist of Farm Service Agency direct loans originated in fiscal years 1994-1996. Models to predict outcomes vary by loan type. Models explaining variation in the financial measures have modest explanatory power but initial levels of debt-to-asset ratio and current ratio are significant in explaining changes in debt-to-asset ratios and current ratios, respectively. Models explaining number of restructurings and delinquencies for operating loans have satisfactory explanatory power. Increasing crop revenues to total farm revenues and increasing farm size lead to increased loan servicing actionsFSA direct loans, financial improvement, loan servicing actions, Agricultural Finance, Farm Management, q14, q12,

Analysis of Participation in Multifunctional Agriculture: U.S. Rice Farms

Multifunctional agriculture is particularly fundamental to some working lands conservation policies and programs, such as the Environmental Quality Incentive Program (EQIP), Conservation Security Program (CSP) and Wildlife Habitat Incentive Program (WHIP). Farmers can also be engaged in providing recreational and agri-tourism services such as hunting, fishing, bird-watching, farm tours, petting zoos and hospitality services. Using the Agricultural Resource Management Survey (ARMS) we analyze factors associated with participation in conservation, recreation and agri-tourism activities as a function of farm structure, farm financial measures, production practices, and socio-demographic characteristics of the farm operator. To estimate the functional relationships we estimate a binary logistic model where the dependent variable takes a value equal to one if the farm operator reports in the ARMS survey participation in conservation programs, recreation or agritourism. Results show that the level of farm operator education and cultural practices that use conservation technical assistance are significant at the 0.01 and 0.10 levels, respectively, in explaining participation. Farm financial characteristics were not significant. Location (state where operator is located) is also not significant.multifunctional agriculture, agri-environmental policy, rice, logistic model, Agricultural and Food Policy, Land Economics/Use, Q18, Q26, Q28,

The LyAlpha Line Profiles of Ultraluminous Infrared Galaxies: Fast Winds and Lyman Continuum Leakage

We present new Hubble Space Telescope Cosmic Origins Spectrograph far-ultraviolet (far-UV) spectroscopy and Keck Echellete optical spectroscopy of 11 ultraluminous infrared galaxies (ULIRGs), a rare population of local galaxies experiencing massive gas inflows, extreme starbursts, and prominent outflows. We detect H Lyman alpha emission from 8 ULIRGs and the companion to IRAS09583+4714. In contrast to the P Cygni profiles often seen in galaxy spectra, the H Lyman alpha profiles exhibit prominent, blueshifted emission out to Doppler shifts exceeding -1000 km/s in three HII-dominated and two AGN-dominated ULIRGs. To better understand the role of resonance scattering in shaping the H Lyman alpha line profiles, we directly compare them to non-resonant emission lines in optical spectra. We find that the line wings are already present in the intrinsic nebular spectra, and scattering merely enhances the wings relative to the line core. The H Lyman alpha attenuation (as measured in the COS aperture) ranges from that of the far-UV continuum to over 100 times more. A simple radiative transfer model suggests the H Lyman alpha photons escape through cavities which have low column densities of neutral hydrogen and become optically thin to the Lyman continuum in the most advanced mergers. We show that the properties of the highly blueshifted line wings on the H Lyman alpha and optical emission-line profiles are consistent with emission from clumps of gas condensing out of a fast, hot wind. The luminosity of the H Lyman alpha emission increases non-linearly with the ULIRG bolometric luminosity and represents about 0.1 to 1% of the radiative cooling from the hot winds in the HII-dominated ULIRGs.Comment: Submitted to Ap