Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy

The assembly of retroviruses such as HIV-1 is driven by oligomerization of their major structural protein, Gag. Gag is a multidomain polyprotein including three conserved folded domains: MA (matrix), CA (capsid) and NC (nucleocapsid)(1). Assembly of an infectious virion proceeds in two stages(2). In the first stage, Gag oligomerization into a hexameric protein lattice leads to the formation of an incomplete, roughly spherical protein shell that buds through the plasma membrane of the infected cell to release an enveloped immature virus particle. In the second stage, cleavage of Gag by the viral protease leads to rearrangement of the particle interior, converting the non-infectious immature virus particle into a mature infectious virion. The immature Gag shell acts as the pivotal intermediate in assembly and is a potential target for anti-retroviral drugs both in inhibiting virus assembly and in disrupting virus maturation(3). However, detailed structural information on the immature Gag shell has not previously been available. For this reason it is unclear what protein conformations and interfaces mediate the interactions between domains and therefore the assembly of retrovirus particles, and what structural transitions are associated with retrovirus maturation. Here we solve the structure of the immature retroviral Gag shell from Mason-Pfizer monkey virus by combining cryo-electron microscopy and tomography. The 8-angstrom resolution structure permits the derivation of a pseudo-atomic model of CA in the immature retrovirus, which defines the protein interfaces mediating retrovirus assembly. We show that transition of an immature retrovirus into its mature infectious form involves marked rotations and translations of CA domains, that the roles of the amino-terminal and carboxy-terminal domains of CA in assembling the immature and mature hexameric lattices are exchanged, and that the CA interactions that stabilize the immature and mature viruses are almost completely distinct.

A novel winding structure in planar inductors to decrease overall capacitive couplings

This paper analyses effects of winding structure on capacitive coupling reduction appearing in the planar magnetic elements at high frequencies. Capacitive coupling appears between the conductive layers of the planar transformers resulting in high current spikes and consequently high power dissipation. With finite element analysis, the equivalent capacitive coupling of magnetic elements is calculated for different structures of planar windings. Finally, a new winding structure with minimum capacitive coupling is introduced for the planar magnetic elements, which is verified by simulation and experiments.

Feasibility of agent-based modelling of articular cartilage including a conceptual representation of its structure

Articular cartilage is a complex structure with an architecture in which fluid-swollen proteoglycans constrained within a 3D network of collagen fibrils. Because of the complexity of the cartilage structure, the relationship between its mechanical behaviours at the macroscale level and its components at the micro-scale level are not completely understood. The research objective in this thesis is to create a new model of articular cartilage that can be used to simulate and obtain insight into the micro-macro-interaction and mechanisms underlying its mechanical responses during physiological function. The new model of articular cartilage has two characteristics, namely: i) not use fibre-reinforced composite material idealization ii) Provide a framework for that it does probing the micro mechanism of the fluid-solid interaction underlying the deformation of articular cartilage using simple rules of repartition instead of constitutive / physical laws and intuitive curve-fitting. Even though there are various microstructural and mechanical behaviours that can be studied, the scope of this thesis is limited to osmotic pressure formation and distribution and their influence on cartilage fluid diffusion and percolation, which in turn governs the deformation of the compression-loaded tissue. The study can be divided into two stages. In the first stage, the distributions and concentrations of proteoglycans, collagen and water were investigated using histological protocols. Based on this, the structure of cartilage was conceptualised as microscopic osmotic units that consist of these constituents that were distributed according to histological results. These units were repeated three-dimensionally to form the structural model of articular cartilage. In the second stage, cellular automata were incorporated into the resulting matrix (lattice) to simulate the osmotic pressure of the fluid and the movement of water within and out of the matrix; following the osmotic pressure gradient in accordance with the chosen rule of repartition of the pressure. The outcome of this study is the new model of articular cartilage that can be used to simulate and study the micromechanical behaviours of cartilage under different conditions of health and loading. These behaviours are illuminated at the microscale level using the socalled neighbourhood rules developed in the thesis in accordance with the typical requirements of cellular automata modelling. Using these rules and relevant Boundary Conditions to simulate pressure distribution and related fluid motion produced significant results that provided the following insight into the relationships between osmotic pressure gradient and associated fluid micromovement, and the deformation of the matrix. For example, it could be concluded that: 1. It is possible to model articular cartilage with the agent-based model of cellular automata and the Margolus neighbourhood rule. 2. The concept of 3D inter connected osmotic units is a viable structural model for the extracellular matrix of articular cartilage. 3. Different rules of osmotic pressure advection lead to different patterns of deformation in the cartilage matrix, enabling an insight into how this micromechanism influences macromechanical deformation. 4. When features such as transition coefficient were changed, permeability (representing change) is altered due to the change in concentrations of collagen, proteoglycans (i.e. degenerative conditions), the deformation process is impacted. 5. The boundary conditions also influence the relationship between osmotic pressure gradient and fluid movement at the micro-scale level. The outcomes are important to cartilage research since we can use these to study the microscale damage in the cartilage matrix. From this, we are able to monitor related diseases and their progression leading to potential insight into drug-cartilage interaction for treatment. This innovative model is an incremental progress on attempts at creating further computational modelling approaches to cartilage research and other fluid-saturated tissues and material systems.

Academic wage structure by gender : the roles of peer review, performance, and market forces

We focus on understanding the role of productivity in determining wage structure differences between men and women in academia. The data arise from a pay-equity study carried out in a single Midwestern U.S. university over the 1996–7 academic year. Econometric results confirm that external market forces exert influence over both male and female salary. But peer review ratings play a significant role in male but not female earnings determination, with similar results for objective measures of research, teaching and service.

Assessment of the molecular structure of the borate mineral sakhaite Ca12Mg4(BO3)7(CO3)4Cl(OH)2·H2O using vibrational spectroscopy

The structure of the borate mineral sakhaite Ca12Mg4(BO3)7(CO3)4Cl(OH)2·H2O, a borate–carbonate of calcium and magnesium has been assessed using vibrational spectroscopy. Assignment of bands is undertaken by comparison with the data from other published results. Intense Raman band at 1134 cm−1 with a shoulder at 1123 cm−1 is assigned to the symmetric stretching mode. The Raman spectrum displays bands at 1479, 1524 and 1560 cm−1 which are assigned to the antisymmetric stretching vibrations. The observation of multiple carbonate stretching bands supports the concept that the carbonate units are non-equivalent. The Raman band at 968 cm−1 with a shoulder at 950 cm−1 is assigned to the symmetric stretching mode of trigonal boron. Raman bands at 627 and 651 cm−1 are assigned to the out-of-plane bending modes of trigonal and tetrahedral boron. Raman spectroscopy coupled with infrared spectroscopy enables the molecular structure of the mineral sakhaite to be assessed.

Assessment of the molecular structure of the borate mineral boracite Mg3B7O13Cl using vibrational spectroscopy

Boracite is a magnesium borate mineral with formula: Mg3B7O13Cl and occurs as blue green, colorless, gray, yellow to white crystals in the orthorhombic – pyramidal crystal system. An intense Raman band at 1009 cm−1 was assigned to the BO stretching vibration of the B7O13 units. Raman bands at 1121, 1136, 1143 cm−1 are attributed to the in-plane bending vibrations of trigonal boron. Four sharp Raman bands observed at 415, 494, 621 and 671 cm−1 are simply defined as trigonal and tetrahedral borate bending modes. The Raman spectrum clearly shows intense Raman bands at 3405 and 3494 cm−1, thus indicating that some Cl anions have been replaced with OH units. The molecular structure of a natural boracite has been assessed by using vibrational spectroscopy.

Aluminosilicates of zeolite N structure

A process for making aluminosilicates of zeolite N structure comprising the steps of: (i) combining a water soluble monovalent cation, a solution of hydroxyl anions and an aluminosilicate to form a resultant mixture having a pH greater than 10 and a H.sub.2O/Al.sub.2O.sub.3 ratio in the range 30 to 220; (ii) heating the resultant mixture to a temperature of between 50.degree. C. and boiling point of the mixture for a time between 1 minute and 100 hours until a crystalline product of zeolite N structure is formed as determined by X-ray diffraction or other suitable characteristic; and (iii) separating the zeolite N product as a solid from the mixture.

Pore structure characterization of North American shale gas reservoirs using USANS/SANS, gas adsorption, and mercury intrusion

Small-angle and ultra-small-angle neutron scattering (SANS and USANS), low-pressure adsorption (N2 and CO2), and high-pressure mercury intrusion measurements were performed on a suite of North American shale reservoir samples providing the first ever comparison of all these techniques for characterizing the complex pore structure of shales. The techniques were used to gain insight into the nature of the pore structure including pore geometry, pore size distribution and accessible versus inaccessible porosity. Reservoir samples for analysis were taken from currently-active shale gas plays including the Barnett, Marcellus, Haynesville, Eagle Ford, Woodford, Muskwa, and Duvernay shales. Low-pressure adsorption revealed strong differences in BET surface area and pore volumes for the sample suite, consistent with variability in composition of the samples. The combination of CO2 and N2 adsorption data allowed pore size distributions to be created for micro–meso–macroporosity up to a limit of �1000 Å. Pore size distributions are either uni- or multi-modal. The adsorption-derived pore size distributions for some samples are inconsistent with mercury intrusion data, likely owing to a combination of grain compression during high-pressure intrusion, and the fact that mercury intrusion yields information about pore throat rather than pore body distributions. SANS/USANS scattering data indicate a fractal geometry (power-law scattering) for a wide range of pore sizes and provide evidence that nanometer-scale spatial ordering occurs in lower mesopore–micropore range for some samples, which may be associated with inter-layer spacing in clay minerals. SANS/USANS pore radius distributions were converted to pore volume distributions for direct comparison with adsorption data. For the overlap region between the two methods, the agreement is quite good. Accessible porosity in the pore size (radius) range 5 nm–10 lm was determined for a Barnett shale sample using the contrast matching method with pressurized deuterated methane fluid. The results demonstrate that accessible porosity is pore-size dependent.

Effect of rehydration on structure and surface properties of thermally treated palygorskite

Palygorskite has a fibrous like morphology with a distinctive layered appearance. The simplified formula of palygorskite (Mg5Si8O20(OH)2(OH2)4 nH2O) indicates that two different types of water are present. The dehydration and rehydration of palygorskite have been studied using thermogravimetry and H2O-tem- perature programmed desorption. X-ray diffractograms, NH3 adsorption profiles, and NH3 desorption profiles were obtained for thermally treated palygorskite as a function of temperature. The results proved water molecules were mainly derived from Si–OH units. In addition, five kinds of acid sites were found for palygorskite. The number of acid sites of external surfaces was larger than that of the internal sur- faces. Bonding on the internal surface acid sites was stronger than the bonding of the external surfaces. Rehydration restored the folded structure of palygorskite when thermal treatment temperature was lower than 300 oC.

The molecular structure of matioliite – NaMgAl5(PO4)4(OH)6·2(H2O) : a pegmatite mineral from Minas Gerais, Brazil

Detailed spectroscopic and chemical investigation of matioliite, including infrared and Raman spectroscopy, scanning electron microscopy and electron probe microanalysis has been carried out on homogeneous samples from the Gentil pegmatite, Mendes Pimentel, Minas Gerais, Brazil. The chemical composition is (wt.%): FeO 2.20, CaO 0.05, Na2O 1.28, MnO 0.06, Al2O3 39.82, P2O5 42.7, MgO 4.68, F 0.02 and H2O 9.19; total 100.00. The mineral crystallize in the monoclinic crystal system, C2/c space group, with a = 25.075(1) Å, b = 5.0470(3) Å, c = 13.4370(7) Å, β = 110.97(3)°, V = 1587.9(4) Å3, Z = 4. Raman spectroscopy coupled with infrared spectroscopy supports the concept of phosphate, hydrogen phosphate and dihydrogen phosphate units in the structure of matioliite. Infrared and Raman bands attributed to water and hydroxyl stretching modes are identified. Vibrational spectroscopy adds useful information to the molecular structure of matioliite.

Characterization of tight gas reservoir pore structure using USANS/SANS and gas adsorption analysis

Small-angle and ultra-small-angle neutron scattering (SANS and USANS) measurements were performed on samples from the Triassic Montney tight gas reservoir in Western Canada in order to determine the applicability of these techniques for characterizing the full pore size spectrum and to gain insight into the nature of the pore structure and its control on permeability. The subject tight gas reservoir consists of a finely laminated siltstone sequence; extensive cementation and moderate clay content are the primary causes of low permeability. SANS/USANS experiments run at ambient pressure and temperature conditions on lithologically-diverse sub-samples of three core plugs demonstrated that a broad pore size distribution could be interpreted from the data. Two interpretation methods were used to evaluate total porosity, pore size distribution and surface area and the results were compared to independent estimates derived from helium porosimetry (connected porosity) and low-pressure N2 and CO2 adsorption (accessible surface area and pore size distribution). The pore structure of the three samples as interpreted from SANS/USANS is fairly uniform, with small differences in the small-pore range (<2000 Å), possibly related to differences in degree of cementation, and mineralogy, in particular clay content. Total porosity interpreted from USANS/SANS is similar to (but systematically higher than) helium porosities measured on the whole core plug. Both methods were used to estimate the percentage of open porosity expressed here as a ratio of connected porosity, as established from helium adsorption, to the total porosity, as estimated from SANS/USANS techniques. Open porosity appears to control permeability (determined using pressure and pulse-decay techniques), with the highest permeability sample also having the highest percentage of open porosity. Surface area, as calculated from low-pressure N2 and CO2 adsorption, is significantly less than surface area estimates from SANS/USANS, which is due in part to limited accessibility of the gases to all pores. The similarity between N2 and CO2-accessible surface area suggests an absence of microporosity in these samples, which is in agreement with SANS analysis. A core gamma ray profile run on the same core from which the core plug samples were taken correlates to profile permeability measurements run on the slabbed core. This correlation is related to clay content, which possibly controls the percentage of open porosity. Continued study of these effects will prove useful in log-core calibration efforts for tight gas.

Dots versus antidots : computational exploration of structure, magnetism, and half-metallicity in boron−nitride nanostructures

Triangle-shaped nanohole, nanodot, and lattice antidot structures in hexagonal boron-nitride (h-BN) monolayer sheets are characterized with density functional theory calculations utilizing the local spin density approximation. We find that such structures may exhibit very large magnetic moments and associated spin splitting. N-terminated nanodots and antidots show strong spin anisotropy around the Fermi level, that is, half-metallicity. While B-terminated nanodots are shown to lack magnetism due to edge reconstruction, B-terminated nanoholes can retain magnetic character due to the enhanced structural stability of the surrounding two-dimensional matrix. In spite of significant lattice contraction due to the presence of multiple holes, antidot super lattices are predicted to be stable, exhibiting amplified magnetism as well as greatly enhanced half-metallicity. Collectively, the results indicate new opportunities for designing h-BNbased nanoscale devices with potential applications in the areas of spintronics, light emission, and photocatalysis.

Conserved and variable features of gag structure and arrangement in immature retrovirus particles

The assembly of retroviruses is driven by oligomerization of the Gag polyprotein. We have used cryo-electron tomography together with subtomogram averaging to describe the three-dimensional structure of in vitro-assembled Gag particles from human immunodeficiency virus, Mason-Pfizer monkey virus, and Rous sarcoma virus. These represent three different retroviral genera: the lentiviruses, betaretroviruses and alpharetroviruses. Comparison of the three structures reveals the features of the supramolecular organization of Gag that are conserved between genera and therefore reflect general principles of Gag-Gag interactions and the features that are specific to certain genera. All three Gag proteins assemble to form approximately spherical hexameric lattices with irregular defects. In all three genera, the N-terminal domain of CA is arranged in hexameric rings around large holes. Where the rings meet, 2-fold densities, assigned to the C-terminal domain of CA, extend between adjacent rings, and link together at the 6-fold symmetry axis with a density, which extends toward the center of the particle into the nucleic acid layer. Although this general arrangement is conserved, differences can be seen throughout the CA and spacer peptide regions. These differences can be related to sequence differences among the genera. We conclude that the arrangement of the structural domains of CA is well conserved across genera, whereas the relationship between CA, the spacer peptide region, and the nucleic acid is more specific to each genus.

Dynamic capabilities and performance : strategy, structure and environment

Dynamic capabilities are widely considered to incorporate those processes that enable organizations to sustain superior performance over time. In this paper, we argue theoretically and demonstrate empirically that these effects are contingent on organizational structure and the competitive intensity in the market. Results from partial least square structural equation modeling (PLS-SEM) analyses indicate that organic organizational structures facilitate the impact of dynamic capabilities on organizational performance. Furthermore, we find that the performance effects of dynamic capabilities are contingent on the competitive intensity faced by firms. Our findings demonstrate the performance effects of internal alignment between organizational structure and dynamic capabilities, as well as the external fit of dynamic capabilities with competitive intensity. We outline the advantages of PLS-SEM for modeling latent constructs, such as dynamic capabilities, and conclude with managerial implications.