Design of an HA2-based Escherichia coli expressed influenza immunogen that protects mice from pathogenic challenge

Influenza HA is the primary target of neutralizing antibodies during infection, and its sequence undergoes genetic drift and shift in response to immune pressure. The receptor binding HA1 subunit of HA shows much higher sequence variability relative to the metastable, fusion-active HA2 subunit, presumably because neutralizing antibodies are primarily targeted against the former in natural infection. We have designed an HA2-based immunogen using a protein minimization approach that incorporates designed mutations to destabilize the low pH conformation of HA2. The resulting construct (HA6) was expressed in Escherichia coli and refolded from inclusion bodies. Biophysical studies and mutational analysis of the protein indicate that it is folded into the desired neutral pH conformation competent to bind the broadly neutralizing HA2 directed monoclonal 12D1, not the low pH conformation observed in previous studies. HA6 was highly immunogenic in mice and the mice were protected against lethal challenge by the homologous A/HK/68 mouse-adapted virus. An HA6-like construct from another H3 strain (A/Phil/2/82) also protected mice against A/HK/68 challenge. Regions included in HA6 are highly conserved within a subtype and are fairly well conserved within a clade. Targeting the highly conserved HA2 subunit with a bacterially produced immunogen is a vaccine strategy that may aid in pandemic preparedness.

Kinetics of copolyurethane network formation

Cure kinetics for the formation of copolyurethane networks of various compositions based on hydroxy-terminated polybutadiene(HTPB), poly(12-hydroxy stearic acid-co-TMP) ester polyol(PEP), and different isocyanates has been studied through viscosity build up during the cure reaction. The viscosity (N)-time (t) plots conform to the equation N = ae(bt), where a and b are empirical constants, dependent on the composition and the nature of the polyols and the isocyanates. The rate constants (b) for viscosity build up, evaluated from the slopes of dN/dt versus N plots at different temperatures, were found to vary significantly from 0.0073 to 0.25 min(-1); and the activation energies for gelation were found to be in the range 20 to 40 kJ mol(-1). The results have been interpreted in terms of the dependence of the rate constants on structural characteristics of the prepolymers. (C) 1997 John Wiley & Sons, Inc.

Examining the effects of species richness on community stability: an assembly model approach

We build dynamic models of community assembly by starting with one species in our model ecosystem and adding colonists. We find that the number of species present first increases, then fluctuates about some level. We ask: how large are these fluctuations and how can we characterize them statistically? As in Robert May's work, communities with weaker interspecific interactions permit a greater number of species to coexist on average. We find that as this average increases, however, the relative variation in the number of species and return times to mean community levels decreases. In addition, the relative frequency of large extinction events to small extinction events decreases as mean community size increases. While the model reproduces several of May's results, it also provides theoretical support for Charles Elton's idea that diverse communities such as those found in the tropics should be less variable than depauperate communities such as those found in arctic or agricultural settings.

Faster Algorithms for Incremental Topological Ordering.Robert Tarjan

We present two online algorithms for maintaining a topological order of a directed acyclic graph as arcs are added, and detecting a cycle when one is created. Our first algorithm takes O(m 1/2) amortized time per arc and our second algorithm takes O(n 2.5/m) amortized time per arc, where n is the number of vertices and m is the total number of arcs. For sparse graphs, our O(m 1/2) bound improves the best previous bound by a factor of logn and is tight to within a constant factor for a natural class of algorithms that includes all the existing ones. Our main insight is that the two-way search method of previous algorithms does not require an ordered search, but can be more general, allowing us to avoid the use of heaps (priority queues). Instead, the deterministic version of our algorithm uses (approximate) median-finding; the randomized version of our algorithm uses uniform random sampling. For dense graphs, our O(n 2.5/m) bound improves the best previously published bound by a factor of n 1/4 and a recent bound obtained independently of our work by a factor of logn. Our main insight is that graph search is wasteful when the graph is dense and can be avoided by searching the topological order space instead. Our algorithms extend to the maintenance of strong components, in the same asymptotic time bounds.

Averting biodiversity collapse in tropical forest protected areas

The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon(1-3). With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses(4-9). As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world's major tropical regions. Our analysis reveals great variation in reserve `health': about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.

RRI-GBT MULTI-BAND RECEIVER: MOTIVATION, DESIGN, AND DEVELOPMENT

We report the design and development of a self-contained multi-band receiver (MBR) system, intended for use with a single large aperture to facilitate sensitive and high time-resolution observations simultaneously in 10 discrete frequency bands sampling a wide spectral span (100-1500 MHz) in a nearly log-periodic fashion. The development of this system was primarily motivated by need for tomographic studies of pulsar polar emission regions. Although the system design is optimized for the primary goal, it is also suited for several other interesting astronomical investigations. The system consists of a dual-polarization multi-band feed (with discrete responses corresponding to the 10 bands pre-selected as relatively radio frequency interference free), a common wide-band radio frequency front-end, and independent back-end receiver chains for the 10 individual sub-bands. The raw voltage time sequences corresponding to 16 MHz bandwidth each for the two linear polarization channels and the 10 bands are recorded at the Nyquist rate simultaneously. We present the preliminary results from the tests and pulsar observations carried out with the Robert C. Byrd Green Bank Telescope using this receiver. The system performance implied by these results and possible improvements are also briefly discussed.

Vorticity moments in four numerical simulations of the 3D Navier-Stokes equations

The issue of intermittency in numerical solutions of the 3D Navier-Stokes equations on a periodic box 0, L](3) is addressed through four sets of numerical simulations that calculate a new set of variables defined by D-m(t) = (pi(-1)(0) Omega(m))(alpha m) for 1 <= m <= infinity where alpha(m) = 2m/(4m - 3) and Omega(m)(t)](2m) = L-3 integral(v) vertical bar omega vertical bar(2m) dV with pi(0) = vL(-2). All four simulations unexpectedly show that the D-m are ordered for m = 1,..., 9 such that Dm+1 < D-m. Moreover, the D-m squeeze together such that Dm+1/D-m NE arrow 1 as m increases. The values of D-1 lie far above the values of the rest of the D-m, giving rise to a suggestion that a depletion of nonlinearity is occurring which could be the cause of Navier-Stokes regularity. The first simulation is of very anisotropic decaying turbulence; the second and third are of decaying isotropic turbulence from random initial conditions and forced isotropic turbulence at fixed Grashof number respectively; the fourth is of very-high-Reynolds-number forced, stationary, isotropic turbulence at up to resolutions of 4096(3).

Regimes of nonlinear depletion and regularity in the 3D Navier-Stokes equations

The periodic 3D Navier-Stokes equations are analyzed in terms of dimensionless, scaled, L-2m-norms of vorticity D-m (1 <= m <= infinity). The first in this hierarchy, D-1, is the global enstrophy. Three regimes naturally occur in the D-1-D-m plane. Solutions in the first regime, which lie between two concave curves, are shown to be regular, owing to strong nonlinear depletion. Moreover, numerical experiments have suggested, so far, that all dynamics lie in this heavily depleted regime 1]; new numerical evidence for this is presented. Estimates for the dimension of a global attractor and a corresponding inertial range are given for this regime. However, two more regimes can theoretically exist. In the second, which lies between the upper concave curve and a line, the depletion is insufficient to regularize solutions, so no more than Leray's weak solutions exist. In the third, which lies above this line, solutions are regular, but correspond to extreme initial conditions. The paper ends with a discussion on the possibility of transition between these regimes.

An estimate of the number of tropical tree species

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between similar to 40,000 and similar to 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of similar to 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of similar to 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.