Solution structure and characterization of the LGR8 receptor binding surface of insulin-like peptide 3

Insulin-like peptide 3 (INSL3), a member of the relaxin peptide family, is produced in testicular Leydig cells and ovarian thecal cells. Gene knock-out experiments have identified a key biological role in initiating testes descent during fetal development. Additionally, INSL3 has an important function in mediating male and female germ cell function. These actions are elicited via its recently identified receptor, LGR8, a member of the leucine-rich repeat-containing G-protein- coupled receptor family. To identify the structural features that are responsible for the interaction of INSL3 with its receptor, its solution structure was determined by NMR spectroscopy together with in vitro assays of a series of B-chain alanine-substituted analogs. Synthetic human INSL3 was found to adopt a characteristic relaxin/ insulin-like fold in solution but is a highly dynamic molecule. The four termini of this two-chain peptide are disordered, and additional conformational exchange is evident in the molecular core. Alanine-substituted analogs were used to identify the key residues of INSL3 that are responsible for the interaction with the ectodomain of LGR8. These include Arg(B16) and Val(B19), with His(B12) and Arg(B20) playing a secondary role, as evident from the synergistic effect on the activity in double and triple mutants involving these residues. Together, these amino acids combine with the previously identified critical residue, Trp(B27), to form the receptor binding surface. The current results provide clear direction for the design of novel specific agonists and antagonists of this receptor.

The effect of rock surface aspect on growth, size structure and competition in the lichen Rhizocarpon geographicum

Rhizocarpon geographicum is a crustose lichen found frequently on rock surfaces of southern aspect and less frequently on rock surfaces of northern aspect in Gwynedd, North Wales. This study tested the hypothesis that the radial growth of R. geographicum thalli predicts aspect distribution. Thalli of all sizes, however, exhibited significantly greater radial growth over 18 months on northwest compared with southeast facing surfaces. The hypothesis that a more intense competitive environment on northwest facing surfaces may explain the aspect distribution of R. geographicum was then tested. The size frequency distributions of thalli revealed a higher proportion of thalli in the smallest size class and a more restricted thallus size range on the northwest facing surfaces. In addition, thallus mortality appeared to be greater on northwest facing surfaces. Significantly more associated lichen species were present on rock surfaces of northern aspect at sites where R. geographicum was present. The mean frequency of the associated lichen species, however, was significantly lower on surfaces of northern aspect where R. geographicum was present. In addition, two common foliose species at these sites were demonstrated experimentally to overgrow thalli of R. geographicum. It is concluded that the growth of R. geographicum over the study period did not predict aspect distribution and that differences in the competitive environments on northwest and southeast surfaces may be an important factor determining aspect distribution. © 2002 Elsevier Science B.V. All rights reserved.

The correlation of structure and electronic properties near the surface of transition metal oxides

The strong couplings between different degrees of freedom are believed to be responsible for novel and complex phenomena discovered in transition metal oxides (TMOs). The physical complexity is directly responsible for their tunability. Creating surfaces/interfaces add an additional ' man-made' twist, approaching the quantum phenomena of correlated materials. ^ The dissertation focused on the structural and electronic properties in proximity of surface of three prototype TMO compounds by using three complementary techniques: scanning tunneling microscopy, angle-resolved photoelectron spectroscopy and low energy electron diffraction, particularly emphasized the effects of broken symmetry and imperfections like defects on the coupling between charge and lattice degrees of freedom. ^ Ca1.5Sr0.5RuO4 is a layered ruthenate with square lattice and at the boundary of magnetic/orbital instability in Ca2-xSrxRuO4. That the substitution of Sr 2+ with Ca2+ causing RuO6 rotation narrows the dxy band width and changes the Fermi surface topology. Particularly, the γ(dxy) Fermi surface sheet exhibited hole-like in Ca1.5Sr0.5RuO4 in contrast to electron-like in Sr2RuO4, showing a strong charge-lattice coupling. ^ Na0.75CoO2 is a layered cobaltite with triangular lattice exhibiting extraordinary thermoelectric properties. The well-ordered CoO2-terminated surface with random Na distribution was observed. However, lattice constants of the surface are smaller than that in bulk. The surface density of states (DOS) showed strong temperature dependence. Especially, an unusual shift of the minimum DOS occurs below 230 K, clearly indicating a local charging effect on the surface. ^ Cd2Re2O7 is the first known pyrochlore oxide superconductor (Tc ∼ 1K). It exhibited an unusual second-order phase transition occurring at TS1 = 200 K and a controversial first-order transition at TS2 = 120 K. While bulk properties display large anomalies at TS1 but rather subtle and sample-dependent changes at TS2, the surface DOS near the EF show no change at T s1 but a substantial increase below TS2---a complete reversal as the signature for the transitions. We argued that crystal imperfections, mainly defects, which were considerably enhanced at the surface, resulted in the transition at TS2. ^

Surface mean flow and turbulence structure in tropical cyclone winds

Hurricanes are one of the deadliest and costliest natural hazards affecting the Gulf coast and Atlantic coast areas of the United States. An effective way to minimize hurricane damage is to strengthen structures and buildings. The investigation of surface level hurricane wind behavior and the resultant wind loads on structures is aimed at providing structural engineers with information on hurricane wind characteristics required for the design of safe structures. Information on mean wind profiles, gust factors, turbulence intensity, integral scale, and turbulence spectra and co-spectra is essential for developing realistic models of wind pressure and wind loads on structures. The research performed for this study was motivated by the fact that considerably fewer data and validated models are available for tropical than for extratropical storms. ^ Using the surface wind measurements collected by the Florida Coastal Monitoring Program (FCMP) during hurricane passages over coastal areas, this study presents comparisons of surface roughness length estimates obtained by using several estimation methods, and estimates of the mean wind and turbulence structure of hurricane winds over coastal areas under neutral stratification conditions. In addition, a program has been developed and tested to systematically analyze Wall of Wind (WoW) data, that will make it possible to perform analyses of baseline characteristics of flow obtained in the WoW. This program can be used in future research to compare WoW data with FCMP data, as gust and turbulence generator systems and other flow management devices will be used to create WoW flows that match as closely as possible real hurricane wind conditions. ^ Hurricanes are defined as tropical cyclones for which the maximum 1-minute sustained surface wind speeds exceed 74 mph. FCMP data include data for tropical cyclones with lower sustained speeds. However, for the winds analyzed in this study the speeds were sufficiently high to assure that neutral stratification prevailed. This assures that the characteristics of those winds are similar to those prevailing in hurricanes. For this reason in this study the terms tropical cyclones and hurricanes are used interchangeably. ^

Surface Mean Flow and Turbulence Structure in Tropical Cyclone Winds

Hurricanes are one of the deadliest and costliest natural hazards affecting the Gulf coast and Atlantic coast areas of the United States. An effective way to minimize hurricane damage is to strengthen structures and buildings. The investigation of surface level hurricane wind behavior and the resultant wind loads on structures is aimed at providing structural engineers with information on hurricane wind characteristics required for the design of safe structures. Information on mean wind profiles, gust factors, turbulence intensity, integral scale, and turbulence spectra and co-spectra is essential for developing realistic models of wind pressure and wind loads on structures. The research performed for this study was motivated by the fact that considerably fewer data and validated models are available for tropical than for extratropical storms. Using the surface wind measurements collected by the Florida Coastal Monitoring Program (FCMP) during hurricane passages over coastal areas, this study presents comparisons of surface roughness length estimates obtained by using several estimation methods, and estimates of the mean wind and turbulence structure of hurricane winds over coastal areas under neutral stratification conditions. In addition, a program has been developed and tested to systematically analyze Wall of Wind (WoW) data, that will make it possible to perform analyses of baseline characteristics of flow obtained in the WoW. This program can be used in future research to compare WoW data with FCMP data, as gust and turbulence generator systems and other flow management devices will be used to create WoW flows that match as closely as possible real hurricane wind conditions. Hurricanes are defined as tropical cyclones for which the maximum 1-minute sustained surface wind speeds exceed 74 mph. FCMP data include data for tropical cyclones with lower sustained speeds. However, for the winds analyzed in this study the speeds were sufficiently high to assure that neutral stratification prevailed. This assures that the characteristics of those winds are similar to those prevailing in hurricanes. For this reason in this study the terms tropical cyclones and hurricanes are used interchangeably.

A New Method for Modeling Free Surface Flows and Fluid-structure Interaction with Ocean Applications

The computational modeling of ocean waves and ocean-faring devices poses numerous challenges. Among these are the need to stably and accurately represent both the fluid-fluid interface between water and air as well as the fluid-structure interfaces arising between solid devices and one or more fluids. As techniques are developed to stably and accurately balance the interactions between fluid and structural solvers at these boundaries, a similarly pressing challenge is the development of algorithms that are massively scalable and capable of performing large-scale three-dimensional simulations on reasonable time scales. This dissertation introduces two separate methods for approaching this problem, with the first focusing on the development of sophisticated fluid-fluid interface representations and the second focusing primarily on scalability and extensibility to higher-order methods.

We begin by introducing the narrow-band gradient-augmented level set method (GALSM) for incompressible multiphase Navier-Stokes flow. This is the first use of the high-order GALSM for a fluid flow application, and its reliability and accuracy in modeling ocean environments is tested extensively. The method demonstrates numerous advantages over the traditional level set method, among these a heightened conservation of fluid volume and the representation of subgrid structures.

Next, we present a finite-volume algorithm for solving the incompressible Euler equations in two and three dimensions in the presence of a flow-driven free surface and a dynamic rigid body. In this development, the chief concerns are efficiency, scalability, and extensibility (to higher-order and truly conservative methods). These priorities informed a number of important choices: The air phase is substituted by a pressure boundary condition in order to greatly reduce the size of the computational domain, a cut-cell finite-volume approach is chosen in order to minimize fluid volume loss and open the door to higher-order methods, and adaptive mesh refinement (AMR) is employed to focus computational effort and make large-scale 3D simulations possible. This algorithm is shown to produce robust and accurate results that are well-suited for the study of ocean waves and the development of wave energy conversion (WEC) devices.

Inertial dissipation method applied to derive turbulent fluxed over the ocean during the Surface of the Ocean, Fluxes and Interactions with the Atmosphere Atlantic Stratocumulus Transition Experiment (SOFIA/ASTEX) and Structure des Echanges Mer-Atmosphere, Proprietes des Heterogeneites Oceaniques: Recherche Experimentale (SEMAPHORE) experiments with low to moderate wind speed

The transfer coefficients for momentum and heat have been determined for 10 m neutral wind speeds (U-10n) between 0 and 12 m/s using data from the Surface of the Ocean, Fluxes and Interactions with the Atmosphere (SOFIA) and Structure des Echanges Mer-Atmosphere, Proprietes des Heterogeneites Oceaniques: Recherche Experimentale (SEMAPHORE) experiments. The inertial dissipation method was applied to wind and pseudo virtual temperature spectra from a sonic anemometer, mounted on a platform (ship) which was moving through the turbulence held. Under unstable conditions the assumptions concerning the turbulent kinetic energy (TKE) budget appeared incorrect. Using a bulk estimate for the stability parameter, Z/L (where Z is the height and L is the Obukhov length), this resulted in anomalously low drag coefficients compared to neutral conditions. Determining Z/L iteratively, a low rate of convergence was achieved. It was concluded that the divergence of the turbulent transport of TKE was not negligible under unstable conditions. By minimizing the dependence of the calculated neutral drag coefficient on stability, this term was estimated at about -0.65Z/L. The resulting turbulent fluxes were then in close agreement with other studies at moderate wind speed. The drag and exchange coefficients for low wind speeds were found to be C-en x 10(3) = 2.79U(10n)(-1) + 0.66 (U-10n < 5.2 m/s), C-en x 10(3) = C-hn x 10(3) = 1.2 (U-10n greater than or equal to 5.2 m/s), and C-dn x 10(3) = 11.7U(10n)(-2) + 0.668 (U-10n < 5.5 m/s), which imply a rapid increase of the coefficient values as the wind decreased within the smooth flow regime. The frozen turbulence hypothesis and the assumptions of isotropy and an inertial subrange were found to remain valid at these low wind speeds for these shipboard measurements. Incorporation of a free convection parameterization had little effect.

On the critical point structure of eigenfunctions belonging to the first nonzero eigenvalue of a genus two closed hyperbolic surface

We develop a method based on spectral graph theory to approximate the eigenvalues and eigenfunctions of the Laplace-Beltrami operator of a compact riemannian manifold -- The method is applied to a closed hyperbolic surface of genus two -- The results obtained agree with the ones obtained by other authors by different methods, and they serve as experimental evidence supporting the conjectured fact that the generic eigenfunctions belonging to the first nonzero eigenvalue of a closed hyperbolic surface of arbitrary genus are Morse functions having the least possible total number of critical points among all Morse functions admitted by such manifolds

Sound radiation characteristics of a box-type structure

The finite element and boundary element methods are employed in this study to investigate the sound radiation characteristics of a box-type structure. It has been shown [T.R. Lin, J. Pan, Vibration characteristics of a box-type structure, Journal of Vibration and Acoustics, Transactions of ASME 131 (2009) 031004-1–031004-9] that modes of natural vibration of a box-type structure can be classified into six groups according to the symmetry properties of the three panel pairs forming the box. In this paper, we demonstrate that such properties also reveal information about sound radiation effectiveness of each group of modes. The changes of radiation efficiencies and directivity patterns with the wavenumber ratio (the ratio between the acoustic and the plate bending wavenumbers) are examined for typical modes from each group. Similar characteristics of modal radiation efficiencies between a box structure and a corresponding simply supported panel are observed. The change of sound radiation patterns as a function of the wavenumber ratio is also illustrated. It is found that the sound radiation directivity of each box mode can be correlated to that of elementary sound sources (monopole, dipole, etc.) at frequencies well below the critical frequency of the plates of the box. The sound radiation pattern on the box surface also closely related to the vibration amplitude distribution of the box structure at frequencies above the critical frequency. In the medium frequency range, the radiated sound field is dominated by the edge vibration pattern of the box. The radiation efficiency of all box modes reaches a peak at frequencies above the critical frequency, and gradually approaches unity at higher frequencies.

Micro-structure differences in kaolinite suspensions

SEM observations of the aqueous suspensions of kaolinite from Birdwood (South Australia) and Georgia (USA) show noticeable differences in number of physical behaviour which has been explained by different microstructure constitution.. Birdwood kaolinite dispersion gels are observed at very low solid loadings in comparison with Georgia KGa-1 kaolinite dispersions which remain fluid at higher solids loading. To explain this behaviour, the specific particle interactions of Birdwood kaolinite, different from interaction in Georgia kaolinite have been proposed. These interactions may be brought about by the presence of nano-bubbles on clay crystal edges and may force clay particles to aggregate by bubble coalescence. This explains the predominance of stair step edge-edge like (EE) contacts in suspension of Birdwood kaolinite. Such EE linked particles build long strings that form a spacious cell structure. Hydrocarbon contamination of colloidal kaolinite particles and low aspect ratio are discussed as possible explanations of this unusual behaviour of Birdwood kaolinite. In Georgia KGa-1 kaolinite dispersions instead of EE contact between platelets displayed in Birdwood kaolinite, most particles have edge to face (EF) contacts building a cardhouse structure. Such an arrangement is much less voluminous in comparison with the Birdwood kaolinite cellular honeycomb structure observed previously in smectite aqueous suspensions. Such structural characteristics of KGa-1 kaolinite particles enable higher solid volume fractions pulps to form before significantly networked gel consistency is attained.

A surface plasmon resonance-based solution affinity assay for heparan sulfate-binding proteins

A surface plasmon resonance-based solution affinity assay is described for measuring the Kd of binding of heparin/heparan sulfate-binding proteins with a variety of ligands. The assay involves the passage of a pre-equilibrated solution of protein and ligand over a sensor chip onto which heparin has been immobilised. Heparin sensor chips prepared by four different methods, including biotin–streptavidin affinity capture and direct covalent attachment to the chip surface, were successfully used in the assay and gave similar Kd values. The assay is applicable to a wide variety of heparin/HS-binding proteins of diverse structure and function (e.g., FGF-1, FGF-2, VEGF, IL-8, MCP-2, ATIII, PF4) and to ligands of varying molecular weight and degree of sulfation (e.g., heparin, PI-88, sucrose octasulfate, naphthalene trisulfonate) and is thus well suited for the rapid screening of ligands in drug discovery applications.

Clypeotheca, a new skeletal structure in scleractinian corals : a potential stress indicator

Physiological responses to environmental stress are increasingly well studied in scleractinian corals. This work reports a new stress-related skeletal structure we term clypeotheca. Clypeotheca was observed in several livecollected common reef-building coral genera and a two to three kya subfossil specimen from Heron Reef, Great Barrier Reef and consists of an epitheca-like skeletal wall that seals over the surface of parts of the corallum in areas of stress or damage. It appears to form from a coordinated process wherein neighboring polyps and adjoining coenosarc seal themselves off from the surrounding environment as they contract and die. Clypeotheca forms from inward skeletal centripetal growth at the edges of corallites and by the merging of flange-like outgrowths that surround individual spines over the surface of the coenosteum. Microstructurally, the merged flanges are similar to upsidedown dissepiments and true epitheca. Clypeotheca is interpreted primarily as a response to stress that may help protect the colony from invasion of unhealthy tissues by parasites or disease by retracting tissues in areas that have become unhealthy for the polyps. Identification of skeletal responses of corals to environmental stress may enable the frequency of certain types of environmental stress to be documented in past environments. Such data may be important for understanding the nature of reef dynamics through intervals of climate change and for monitoring the effects of possible anthropogenic stress in modern coral reef habitats.