A study to develop neutron activation for measuring bone calcium content

Neutron activation analysis for measuring calcium in monkey bone

Computational design of catalytically active TIM barrel xylanases

TIM barrel enzymes perform five out of six Enzyme Commission (EC) reaction classes, and are therefore one of the most promising class of enzymes for computational design. Up until now, chimeric TIM barrels were made out of half barrels and catalytic activity was installed using laborious rounds of random mutagenesis, selection and rational design, whereas a recently described de novo designed TIM barrel lacked the elaborate loop conformations necessary to install catalytic activity, and indeed did not show activity. In order to design catalytically active TIM barrel glycoside-hydrolase 10 family xylanases, we sampled diverse protein backbone conformations, in some cases generating completely new combinations of backbones at all eight beta-alpha blades, and optimized the sequence for both protein stability and catalytic activity. We then selected structurally diverse, low energy subset of the designs for further characterization. Designs had \u3c60% sequence identity to natural xylanases, incorporating many insertions and deletions in loop regions. All designs expressed well and 30% showed catalytic activity, the most active one having Kcat/Km = 106. The design process samples extensively the sequence-structure space and the designs can serve as a library for altered enzyme selectivity. Moreover, our algorithm is general and robust, and can be applied to other TIM barrel enzyme families having a few dozen solved structures and to other modular protein folds

A minimum principle for superharmonic functions subject to interface conditions

AbstractLet D be a bounded domain in R2 with smooth boundary. Let B1, …, Bm be non-intersecting smooth Jordan curves contained in D, and let D′ denote the complement of ∪i − 1m Bi respect to D. Suppose that u ϵ C2(D′) ∩ C(D̄) and Δu ⩽ 0 in D′ (where Δ is the Laplacian), while across each “interface” Bi, i = 1,…, m, there is “continuity of flux” (as suggested by the theory of heat conduction). It is proved here that the presence of the interfaces does not alter the conclusions of the classical minimum principle (for Δu ⩽ 0 in D). The result is extended in several regards. Also it is applied to an elliptic free boundary problem and to the proof of uniqueness for steady-state heat conduction in a composite medium. Finally this minimum principle (which assumes “continuity of flux”) is compared with one due to Collatz and Werner which employs an alternative interface condition

Projecting current and future location, quality, and connectivity of habitat for breeding birds in the Great Basin

We estimated the current location, quality, and connectivity of habitat for 50 species of breeding birds in four mountain ranges in the central Great Basin (Lander, Nye, and Eureka Counties, Nevada) and projected the future location, quality, and connectivity of habitat for these species given different scenarios of climate-induced land-cover change. In the United States, such models are relevant to federally mandated management of wild animals by state-level agencies. We sampled birds during the breeding seasons of 2001-2009 with fixed-radius point counts. For each species, we used boosted regression trees to model incidence (proportion of years a location was surveyed in which the species was present) as a function of topography and current land cover and climate. To assess model fit, we calculated the proportion of binomial deviance explained. We used cross-validation to estimate the predictive accuracy of the models. We applied the conservation planning program Zonation to identify locations where incidences of multiple species were maximized through time given current land cover and two scenarios of land-cover change, expansion of pinyon-juniper woodland into sagebrush shrubsteppe and contraction of riparian woodland. Models based on a set of 13 covariates derived from remotely sensed data had some predictive capacity for 41 of 50 species. Model outputs suggested substantial changes in amount of habitat for many species following projected expansion of pinyon-juniper woodland, but less pronounced changes following projected contraction of riparian woodland. Zonation analyses indicated that the spatial distribution of the highest-quality habitat for the avian assemblage was relatively consistent through time under both scenarios. Breeding birds in the Great Basin commonly are grouped in management plans on the basis of their general association with land-cover classes such as pinyon-juniper woodland, sagebrush shrubsteppe, and riparian woodland. However, even within these groups, the environmental attributes that explained a high proportion of variation in species\u27 incidences and the projected responses to different scenarios of land-cover change varied considerably among species

Development of tests for measurement of primary perceptual-motor performance

Tests for measuring primary perceptual-motor performance for assessing space environment effects on human performanc

Jitter radiation images, spectra, and light curves from a relativistic spherical blastwave

We consider radiation emitted by the jitter mechanism in a Blandford-McKee self-similar blastwave. We assume the magnetic field configuration throughout the whole blastwave meets the condition for the emission of jitter radiation and we compute the ensuing images, light curves and spectra. The calculations are performed for both a uniform and a wind environment. We compare our jitter results to synchrotron results. We show that jitter radiation produces slightly different spectra than synchrotron, in particular between the self-absorption and the peak frequency, where the jitter spectrum is flat, while the synchrotron spectrum grows as \nu^{1/3}. The spectral difference is reflected in the early decay slope of the light curves. We conclude that jitter and synchrotron afterglows can be distinguished from each other with good quality observations. However, it is unlikely that the difference can explain the peculiar behavior of several recent observations, such as flat X-ray slopes and uncorrelated optical and X-ray behavior.Comment: 11 pages, 7 postscript figures. Accepted for publication in MNRA

Projecting current and future location, quality, and connectivity of habitat for breeding birds in the Great Basin

We estimated the current location, quality, and connectivity of habitat for 50 species of breeding birds in four mountain ranges in the central Great Basin (Lander, Nye, and Eureka Counties, Nevada) and projected the future location, quality, and connectivity of habitat for these species given different scenarios of climate-induced land-cover change. In the United States, such models are relevant to federally mandated management of wild animals by state-level agencies. We sampled birds during the breeding seasons of 2001–2009 with fixed-radius point counts. For each species, we used boosted regression trees to model incidence (proportion of years a location was surveyed in which the species was present) as a function of topography and current land cover and climate. To assess model fit, we calculated the proportion of binomial deviance explained. We used cross-validation to estimate the predictive accuracy of the models. We applied the conservation planning program Zonation to identify locations where incidences of multiple species were maximized through time given current land cover and two scenarios of land-cover change, expansion of pinyon–juniper woodland into sagebrush shrubsteppe and contraction of riparian woodland. Models based on a set of 13 covariates derived from remotely sensed data had some predictive capacity for 41 of 50 species. Model outputs suggested substantial changes in amount of habitat for many species following projected expansion of pinyon–juniper woodland, but less pronounced changes following projected contraction of riparian woodland. Zonation analyses indicated that the spatial distribution of the highest-quality habitat for the avian assemblage was relatively consistent through time under both scenarios. Breeding birds in the Great Basin commonly are grouped in management plans on the basis of their general association with land-cover classes such as pinyon–juniper woodland, sagebrush shrubsteppe, and riparian woodland. However, even within these groups, the environmental attributes that explained a high proportion of variation in species' incidences and the projected responses to different scenarios of land-cover change varied considerably among species

the american naturalist january

abstract: We tested the prediction of the sensory drive hypothesis using four allopatric populations of the lizard Anolis cristatellus from two distinct environments (i.e., mesic and xeric conditions). For each population, we measured habitat light characteristics and quantified signal design by measuring the spectral and total reflectance and transmittance of the dewlap. We used these data to calculate dewlap detectability using an empirically based model of signal detection probability. We found that populations from mesic and xeric conditions occupy two distinct habitats with respect to light intensity and spectral quality and that dewlap design has diverged between populations in a way that increases signal detectability in each habitat. The major difference in dewlap design was in total reflectance and transmittance, making dewlaps from xeric habitats darker and dewlaps from mesic habitats brighter. Furthermore, dewlap detection decreased significantly when a dewlap from a xeric habitat is detected under the spectral conditions of a mesic habitat. The converse is true for a dewlap from a mesic habitat. We propose that sensory drive has promoted divergence in dewlap design in distinct habitat light conditions, and we discuss the possibility that selection might promote early stages of reproductive isolation as a by-product of selection on dewlap design to distinct habitat light conditions. Keywords: Anolis, sensory drive, speciation, natural selection, signal detectability, population divergence. Animals communicate with an amazing variety of signals, and even closely related species often exhibit great signal diversity. A number of studies suggest that divergence i

A combined computational-experimental approach to define the structural origin of antibody recognition of sialyl-Tn, a tumor-associated carbohydrate antigen.

Anti-carbohydrate monoclonal antibodies (mAbs) hold great promise as cancer therapeutics and diagnostics. However, their specificity can be mixed, and detailed characterization is problematic, because antibody-glycan complexes are challenging to crystallize. Here, we developed a generalizable approach employing high-throughput techniques for characterizing the structure and specificity of such mAbs, and applied it to the mAb TKH2 developed against the tumor-associated carbohydrate antigen sialyl-Tn (STn). The mAb specificity was defined by apparent KD values determined by quantitative glycan microarray screening. Key residues in the antibody combining site were identified by site-directed mutagenesis, and the glycan-antigen contact surface was defined using saturation transfer difference NMR (STD-NMR). These features were then employed as metrics for selecting the optimal 3D-model of the antibody-glycan complex, out of thousands plausible options generated by automated docking and molecular dynamics simulation. STn-specificity was further validated by computationally screening of the selected antibody 3D-model against the human sialyl-Tn-glycome. This computational-experimental approach would allow rational design of potent antibodies targeting carbohydrates