An atomic model of the outer layer of the bluetongue virus core derived from X-ray crystallography and electron cryomicroscopy

BACKGROUND: Bluetongue virus (BTV), which belongs to the Reoviridae family and orbivirus genus, is a non-enveloped, icosahedral, double-stranded RNA virus. Several protein layers enclose its genome; upon cell entry the outer layer is stripped away leaving a core, the surface of which is composed of VP7. The structure of the trimeric VP7 molecule has previously been determined using X-ray crystallography. The articulated VP7 subunit consists of two domains, one which is largely alpha-helical and the other, smaller domain, is a beta barrel with jelly-roll topology. The relative orientations of these two domains vary in different crystal forms. The structure of VP7 and the organizations of 780 subunits of this molecule in the core of virus is central to the assembly and function of BTV. RESULTS: A 23 A resolution map of the core, determined using electron cryomicroscopy (cryoEM) data, reveals that the 260 trimers of VP7 are organized on a rather precise T = 13 laevo icosahedral lattice, in accordance with the theory of quasi-equivalence. The VP7 layer occupies a shell that is between 260 A and 345 A from the centre of the core. Below this radius (230-260 A) lies the T = 1 layer of 120 molecules of VP3. By fitting the X-ray structure of an individual VP7 trimer onto the cryoEM BTV core structure, we have generated an atomic model of the VP7 layer of BTV. This demonstrates that one of the molecular structures seen in crystals of the isolated VP7 corresponds to the in vivo conformation of the molecule in the core. CONCLUSIONS: The beta-barrel domains of VP7 are external to the core and interact with protein in the outer layer of the mature virion. The lower, alpha-helical domains of VP7 interact with VP3 molecules which form the inner layer of the BTV core. Adjacent VP7 trimer-trimer interactions in the T = 13 layer are mediated principally through well-defined regions in the broader lower domains, to form a structure that conforms well with that expected from the theory of quasi-equivalence with no significant conformational changes within the individual trimers. The VP3 layer determines the particle size and forms a rather smooth surface upon which the two-dimensional lattice of VP7 trimers is laid down.     

Interleaving solving and elicitation of constraint satisfaction problems based on expected cost

We consider Constraint Satisfaction Problems in which constraints can be initially incomplete, where it is unknown whether certain tuples satisfy the constraint or not. We assume that we can determine the satisfaction of such an unknown tuple, i.e., find out whether this tuple is in the constraint or not, but doing so incurs a known cost, which may vary between tuples. We also assume that we know the probability of an unknown tuple satisfying a constraint. We define algorithms for this problem, based on backtracking search. Specifically, we consider a simple iterative algorithm based on a cost limit on the unknowns that may be determined, and a more complex algorithm that delays determining an unknown in order to estimate better whether doing so is worthwhile. We show experimentally that the more sophisticated algorithms can greatly reduce the average cost.     

Accommodation of impurities in α-Al2O3, α-Cr2O3 and α-Fe2O3

Atomic scale computer simulation was used to predict the mechanisms and energies associated with the accommodation of aliovalent and isovalent dopants in three host oxides with the corundum structure. Here we consider a much more extensive range of dopant ions than has previously been the case. This enables a rigorous comparison of calculated mechanism energetics. From this we predict that divalent ions are charge compensated by oxygen vacancies and tetravalent ions by cation vacancies over the full range of dopant radii. When defect associations are included in the model these conclusions remain valid. At equilibrium, defects resulting from extrinsic dopant solution dominate intrinsic processes, except for the largest dopant cations. Solution reaction energies increase markedly with increasing dopant radius. The behaviour of cluster binding energies is more complex.     

Quantification of multiple bioagents with wireless, remote-query magnetoelastic microsensors

This paper presents a micromagnetoelastic sensor array for simultaneously monitoring multiple biological agents. Magnetoelastic sensors, made of low-cost amorphous ferromagnetic ribbons, are analogous and complementary to piezoelectric acoustic wave sensors, which track parameters of interest via changes in resonance behavior. Magnetoelastic sensors are excited with magnetic ac fields, and, in turn, they generate magnetic fluxes that can be detected with a sensing coil from a distance. As a result, these sensors are highly attractive, not only due to their small size and low cost, but also because of their passive and wireless nature. Magnetoelastic sensors have been applied for monitoring pressure, temperature, liquid density, and viscosity, fluid How velocity and direction, and with chemical/biological responsive coatings that change mass or elasticity, various biological and chemical agents. In this paper, we report the fabrication and application of a six-sensor array for simultaneous measurement of Escherichia coli O157:H7, staphylococcal enterotoxin B, and ricin. In addition, the sensor array also monitors temperature and pH so the measurements are independent from these two parameters.     

Serotonin-1B receptor activity and expression modulate the aggression-stimulating effects of adolescent anabolic steroid exposure in hamsters.

Repeated high dose (5.0 mg/kg) anabolic-androgenic steroid (AAS) exposure during adolescence stimulates offensive aggression in male Syrian hamsters. These studies examined whether AAS-induced aggression was regulated by the activity of serotonin (5HT) type-1B receptors and correlated with altered 5HT1B expression. AAS-treated hamsters were tested for offensive aggression following the administration of the 5HT1B agonist anpirtoline (0.125-0.5 mg/kg). Anpirtoline dose-dependently reduced select components of the AAS-induced aggressive response, with significant reductions observed at 0.25 mg/kg. Aggressive, AAS-treated hamsters showed significant decreases in the area covered by 5HT1B-containing neuronal puncta and increases in the number of 5HT1B-containing neuronal somata in select brain regions implicated in aggression control. Together, these data support a role for site-specific alterations in 5HT1B signaling and expression in adolescent AAS-induced aggression. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Performance comparison of the CRAY X-MP/24 with SDD and the CRAY-2

The CRAY-2 is considered to be one of the most powerful supercomputers. Its state-of-the-art technology features a faster clock and more memory than any other supercomputer available today. In this report the single processor performance of the CRAY-2 is compared with the older, more mature CRAY X-MP. Benchmark results are included for both the slow and the fast memory DRAM MOS CRAY-2. Our comparison is based on a kernel benchmark set aimed at evaluating the performance of these two machines on some standard tasks in scientific computing. Particular emphasis is placed on evaluating the impact of the availability of large real memory on the CRAY-2 versus fast secondary memory on the CRAY X-MP with SSD. Our benchmark includes large linear equation solvers and FFT routines, which test the capabilities of the different approaches to providing large memory. We find that in spite of its higher processor speed the CRAY-2 does not perform as well as the CRAY X-MP on the Fortran kernel benchmark. We also find that for large-scale applications, which have regular and predictable memory access patterns, a high-speed secondary memory device such as the SSD can provide performance equal to the large real memory of the CRAY-2.The author is an employee of SCA Division of Boeing Computer Services.     

Partial least squares analysis of near-infrared hyperspectral images for beef tenderness prediction

Tenderness is a primary determinant of consumer satisfaction of beef steaks. The objective of this study was to implement and test near-infrared (NIR) hyperspectral imaging to forecast 14-day aged, cooked beef tenderness from the hyperspectral images of fresh ribeye steaks (n = 319) acquired at 3–5 day post-mortem. A pushbroom hyperspectral imaging system (wavelength range: 900–1700 nm) with a diffuse-flood lighting system was developed. After imaging, steaks were vacuum-packaged and aged until 14 days postmortem. After aging, the samples were cooked and slice shear force (SSF) values were collected as a tenderness reference. After reflectance calibration, a Region-of-Interest (ROI) of 150 × 300 pixels at the center of longissimus muscle was selected. Partial least squares regression (PLSR) was carried out on each ROI image to reduce the dimension along the spectral axis. Gray-level textural co-occurrence matrix analysis with two quantization levels (64 and 256) was conducted on the PLSR bands to extract second-order statistical textural features. These features were then used in a canonical discriminant model to predict three beef tenderness categories, namely tender (SSF ≤ 205.80 N), intermediate (205.80 N < SSF < 254.80 N), and tough (SSF ≥ 254.80 N). The model with a quantization level of 256 performed better than the one with a quantization level of 64. This model correctly classified 242 out of 314 samples with an overall accuracy of 77.0%. Fat, protein, and water absorption bands were identified between 900 and 1700 nm. Our results show that NIR hyperspectral imaging holds promise as an instrument for forecasting beef tenderness.