Accuracy of the Kirchoff formula in determining acoustic shielding with the use of a flat plate

It has been suggested that if jet engines of aircraft were placed at above the wing instead of below it, the wing would provide a partial shielding of the noise generated by the engines relative to observers on the ground. The shielding effects of an idealized three-dimensional barrier in the presence of an idealized engine noise source was predicted by the Kirchoff formula. Based on the good agreement between experimental measurements and the numerical results of the current study, it was concluded that the Kirchoff approximation provides a good qualitative estimate of the acoustic shielding of a point source by a rectangular flat plate for measurements taken in the far field of the flat plate at frequencies ranging from 1 kHz to 20 kHz. At frequencies greater than 4 kHz the Kirchoff approximation provides accurate quantitative predictions of acoustic shielding

Validation of water flux and body composition in Glaucous gulls (Larus hyperboreus)

Water influx rates (WIR) measured with tritiated water dilution were compared with direct measures of water and energy intake in glaucous gulls (Larus hyperboreus). Total body water (TBW) measured isotopically was also compared with TBW determined by body composition analysis (BCA) of the same birds. Seventeen wild gulls were captured and studied in outdoor enclosures at Ny-Ålesund, Svalbard, in July 2002. Gulls were hand-fed known quantities of Arctic cod (Boreogadus saida) or given water on the basis of one of four experimental treatments: (A) fasting, (B) fish only, (C) water only, or (D) fish and water. Water and energy content of Arctic cod was also determined. WIR of gulls (after subtracting metabolic water production) in treatments A, B, C, and D were 0, 101 ± 5, 62 ± 19, and 122 ± 21 SD g d-1, respectively. Measured water intake in each group was 0, 111 ± 2, 64 ± 3, and 134 ± 15 SD g d-1, respectively. On average, WIR underestimated measured water intake in each group. Errors were lowest but most variable for gulls fed water only (-2.2% ± 32.8%) compared with gulls fed fish only (-9.0% ± 5.4%) or fish and water (-9.0% ± 7.0%). Compared with measured water intake, errors in WIR were relatively low overall (-6.9% ± 17.4%) and comparable to previous validation studies. The difference in TBW determined by BCA versus isotopic dilution ranged between -1.02% and +8.59% of mass. On average, TBW measured isotopically (632 ± 24 g kg-1) overestimated true body water by a factor of 1.033

The structure of an orthorhombic crystal form of a 'forced reduced' thiol peroxidase reveals lattice formation aided by the presence of the affinity tag

Thiol peroxidase (Tpx) is an atypical 2-Cys peroxiredoxin, which has been suggested to be important for cell survival and virulence in Gram-negative pathogens. The structure of a catalytically inactive version of this protein in an orthorhombic crystal form has been determined by molecular replacement. Structural alignments revealed that Tpx is conserved. Analysis of the crystal packing shows that the linker region of the affinity tag is important for formation of the crystal lattice

FolX from Pseudomonas aeruginosa is octameric in both crystal and solution

FolX encodes an epimerase that forms one step of the tetrahydrofolate biosynthetic pathway, which is of interest as it is an established target for important drugs. Here we report the crystal structure of FolX from the bacterial opportunistic pathogen Pseudomonas aeruginosa, as well as a detailed analysis of the protein in solution, using analytical ultracentrifugation (AUC) and small-angle X-ray scattering (SAXS). In combination, these techniques confirm that the protein is an octamer both in the crystal structure, and in solution

Alkali-Labile Cell-Wall Phenolics and Forage Quality in Switchgrasses Selected for Differing Digestibility

Alkali-labile cell-wall phenolics have been implicated in previous research as factors that affect forage digestibility by ruminants. Alkali- labile cell-wall phenolics, in vitro dry matter digestibility (IVDMD), neutral-detergent fiber (NDF), acid-detergent fiber (ADF), lignin (permanganate-oxidation), and crude protein (CP) were determined in three switchgrass (Panicum virgatum L.) strains differing genetically for IVDMD to determine relationships between • these quality parameters and IVDMD during the grazing season. Grazed (upper 1/3 of grazed plants) and ungrazed (whole plants in caged exclosures) forage was collected weekly from replicated 0.4- ha pastures of \u27Trailblazer\u27 (high IVDMD), \u27Pathfinder\u27, and a low- IVDMD strain during three grazing seasons from 1983 to 1985. The principal alkali-labile phenolics (g kg-1 NDF) detected were p-coumaric acid (PCA) and ferulic acid (FA). Increased PCA concentration due to increased maturity averaged \u3e70°/o during each grazing season and corresponded with increased NDF, ADF, and lignin and decreased IVDMD, CP, and FA/PCA ratio. Ferulic acid concentration either declined slightly or remained unchanged. Averaged across 3 yr, Trailblazer had higher (P \u3c 0.06) IVDMD, lower (P \u3c 0.09) PCA and higher (P \u3c 0.10) FA/PCA ratio than a divergently selected low-IVDMD strain. Differences between strains in detergent-fiber constituents, FA, and CP were either not apparent or inconsistent with strain differences in IVDMD. Results were consistent with both grazed and ungrazed switchgrass and indicate that alkali-labile cell-wall phenolic composition in switchgrass is heritable and genetically correlated to IVDMD

A general strategy for discovery of inhibitors and activators of RING and U-box E3 ligases with ubiquitin variants

RING and U-box E3 ubiquitin ligases regulate diverse eukaryotic processes and have been implicated in numerous diseases, but targeting these enzymes remains a major challenge. We report the development of three ubiquitin variants (UbVs), each binding selectively to the RING or U-box domain of a distinct E3 ligase: monomeric UBE4B, phosphorylated active CBL, or dimeric XIAP. Structural and biochemical analyses revealed that UbVs specifically inhibited the activity of UBE4B or phosphorylated CBL by blocking the E2∼Ub binding site. Surprisingly, the UbV selective for dimeric XIAP formed a dimer to stimulate E3 activity by stabilizing the closed E2∼Ub conformation. We further verified the inhibitory and stimulatory functions of UbVs in cells. Our work provides a general strategy to inhibit or activate RING/U-box E3 ligases and provides a resource for the research community to modulate these enzymes

Polarized cell motility induces hydrogen peroxide to inhibit cofilin via cysteine oxidation

Mesenchymal cell motility is driven by polarized actin polymerization [1]. Signals at the leading edge recruit actin polymerization machinery to promote membrane protrusion, while matrix adhesion generates tractive force to propel forward movement. To work effectively, cell motility is regulated by a complex network of signaling events that affect protein activity and localization. H2O2 has an important role as a diffusible second messenger [2], and mediates its effects through oxidation of cysteine thiols. One cell activity influenced by H2O2 is motility [3]. However, a lack of sensitive and H2O2-specific probes for measurements in live cells has not allowed for direct observation of H2O2 accumulation in migrating cells or protrusions. In addition, the identities of proteins oxidized by H2O2 that contribute to actin dynamics and cell motility have not been characterized. We now show, as determined by fluorescence lifetime imaging microscopy, that motile cells generate H2O2 at membranes and cell protrusions and that H2O2 inhibits cofilin activity through oxidation of cysteines 139 (C139) and 147 (C147). Molecular modeling suggests that C139 oxidation would sterically hinder actin association, while the increased negative charge of oxidized C147 would lead to electrostatic repulsion of the opposite negatively charged surface. Expression of oxidation-resistant cofilin impairs cell spreading, adhesion, and directional migration. These findings indicate that H2O2 production contributes to polarized cell motility through localized cofilin inhibition and that there are additional proteins oxidized during cell migration that might have similar roles

Diversity in the structures and ligand binding sites of nematode fatty acid and retinol binding proteins revealed by Na-FAR-1 from Necator americanus

Fatty acid and retinol binding proteins (FARs) comprise a family of unusual α-helix rich lipid binding proteins found exclusively in nematodes. They are secreted into host tissues by parasites of plants, animals and humans. The structure of a FAR protein from the free-living nematode Caenorhabditis elegans is available, but this protein (Ce-FAR-7) is from a subfamily of FARs that does not appear to be important at the host-parasite interface. We have therefore examined Na-FAR-1 from the blood-feeding intestinal parasite of humans, Necator americanus . The three dimensional structure of Na-FAR-1 in its ligand-free and ligand-bound forms, determined by nuclear magnetic resonance spectroscopy (NMR) and X-ray crystallography, respectively, reveals an a-helical fold similar to Ce-FAR-7, but Na-FAR-1 possesses a larger and more complex internal ligand binding cavity and an additional C-terminal a-helix. Titration of apo -Na-FAR-1 with oleic acid, analysed by NMR chemical shift perturbation, reveals that at least four distinct protein:ligand complexes can be formed. Na-FAR-1, and possibly other FARs, may have a wider repertoire for hydrophobic ligand binding, as confirmed here by our finding that a range of neutral and polar lipids co-purify with the bacterial recombinant protein. Finally, we show by immunohistochemistry that Na-FAR-1 is present in adult worms with a tissue distribution indicative of possible roles in nutrient acquisition by the parasite and in reproduction in the male

Self-interaction chromatography as a tool for optimizing conditions for membrane protein crystallization

The second virial coefficient, or B value, is a measurement of how well a protein interacts with itself in solution. These interactions can lead to protein crystallization or precipitation, depending on their strength, with a narrow range of B values (the `crystallization slot') being known to promote crystallization. A convenient method of determining the B value is by self-interaction chromatography. This paper describes how the light-harvesting complex 1-reaction centre core complex from Allochromatium vinosum yielded single straight-edged crystals after iterative cycles of self-interaction chromatography and crystallization. This process allowed the rapid screening of small molecules and detergents as crystallization additives. Here, a description is given of how self-interaction chromatography has been utilized to improve the crystallization conditions of a membrane protein