Selenium Content in Blood Fractions and Liver of Beef Heifers Is Greater with a Mix of Inorganic/Organic or Organic Versus Inorganic Supplemental Selenium but the Time Required for Maximal Assimilation Is Tissue-Specific

Selenium (Se) content of feedstuffs is dependent on the Se level of the soil. Even though Se in grass and forage crops is primarily present in organic forms, Se is commonly supplemented in cattle diets in an inorganic (sodium selenite) form in geographic regions where Se soil concentrations are low. The purpose of this study was to answer two important questions about inorganic (ISe) vs organic (OSe) forms of dietary supplementation of Se (3?mg/day) to growing beef heifers (0.5?kg/day): (1) what would the effect of supplementing Se with an equal blend of ISe:OSe (Mix) have on Se tissue concentrations and (2) how long does it take for the greater assimilation with OSE to occur and stabilize? A long-term (224?day) Se dietary supplementation trial was conducted with serial sampling performed (days?28, 56, 112, and 224) to determine the length of time required to achieve Se supplement (OSE, Mix, and ISe)-dependent changes in Se assimilation in blood fractions and liver tissue. Forty maturing Angus heifers were fed a corn silage-based diet for 98?days with no Se supplementation, and then a cracked corn/cottonseed hull-based diet (basal diet) without Se supplementation for 74?days. Liver biopsies were taken for Se analysis, and heifers were fed the same diet for another 14?days. Heifers were assigned (n?=?10) to one of four Se treatment groups such that basal liver Se contents were stratified among groups, and then fed enough of the basal diet (0.08?mg Se per day) and a mineral-vitamin mix that provided 0.16 (control) or 3.0?mg Se per day in ISe (sodium selenite), OSe (Sel-Plex(?)), or Mix (1:1 ISe:OSe) form to support 0.5?kg/day growth for 224?days. More Se was found in whole blood, red blood cells, serum, and liver of Mix and OSe heifers than ISe heifers, and all were greater than control. Se content either increased until day?56 then was stable (liver and plasma), or was stable until day?56 (whole blood) or day?112 (red blood cells) and then increased steadily through day?224, for all supplemental Se treatments. These data indicate that a 1:1 mix (1.5?mg Se:1.5?mg Se) of supplemental ISe and OSe is equal to 3?mg/day OSe supplementation and greater than 3?mg/day ISe supplementation. The data also indicate that Se levels stabilized in liver and plasma by 56 to 112?days whereas whole blood and red blood cell concentrations were still increasing through 224?days of supplementation, regardless of the form of supplemental Se.     

Predicting spatial occurrence of beetles and pseudoscorpions in hollow oaks in southeastern Sweden

We modelled presence/absence per tree of beetles and pseudoscorpions living in tree hollows in relation to trunk circumference, habitat openness, and connectivity (= density of hollow oaks in the surrounding area), using data from 281 oaks. The presence/absence models were then used to predict species’ occurrences in a county (11,600 km²) in southeastern Sweden. For eight of the nine species, the most parsimonious occupancy model included a positive relationship with connectivity and at least one tree characteristic. Occupancy underestimates from occurrence records—the ratio of the area of occupancy based on our predictive model to the area of occupancy based on occurrence records—varied between 3 and 83 among species when using occurrence records up to 1993, with significantly larger underestimates for smaller beetle species. Today (after extensive surveys), underestimation has decreased to 1.3–25, confirming that calculations solely based on species occurrence records greatly underestimate the area of occupancy. We suggest this should be taken into account to a greater extent and in a clearer way than today when constructing red lists. The radius of the connectivity measure that generated the best fit varied between 135 and 2,857 m among species, with longer distances for more threatened species. Consequently, preservation of the most threatened species (Elater ferrugineus and Tenebrio opacus) requires conservation efforts at larger spatial scales than required to protect Osmoderma eremita, which frequently has been used as an indicator and umbrella species.     

Investigation of the mode of binding of a novel series of N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamides to the hepatitis C virus polymerase

Structure based rationales for the activities of potent N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamide inhibitors of the hepatitis C viral polymerase are described herein. These compounds bind to the hepatitis C virus non-structural protein 5B (NS5B), and co-crystal structures of select examples from this series with NS5B are reported. Comparison of co-crystal structures of a potent analog with both NS5B genotype 1a and genotype 1b provides a possible explanation for the genotype-selectivity observed with this compound class and suggests opportunities for the further optimization of the series.     

A large-scale forest fragmentation experiment: the Stability of Altered Forest Ecosystems Project

Opportunities to conduct large-scale field experiments are rare, but provide a unique opportunity to reveal the complex processes that operate within natural ecosystems. Here, we review the design of existing, large-scale forest fragmentation experiments. Based on this review, we develop a design for the Stability of Altered Forest Ecosystems (SAFE) Project, a new forest fragmentation experiment to be located in the lowland tropical forests of Borneo (Sabah, Malaysia). The SAFE Project represents an advance on existing experiments in that it: (i) allows discrimination of the effects of landscape-level forest cover from patch-level processes; (ii) is designed to facilitate the unification of a wide range of data types on ecological patterns and processes that operate over a wide range of spatial scales; (iii) has greater replication than existing experiments; (iv) incorporates an experimental manipulation of riparian corridors; and (v) embeds the experimentally fragmented landscape within a wider gradient of land-use intensity than do existing projects. The SAFE Project represents an opportunity for ecologists across disciplines to participate in a large initiative designed to generate a broad understanding of the ecological impacts of tropical forest modification.     

Do Roads Reduce Painted Turtle (Chrysemys picta) Populations?

Road mortality is thought to be a leading cause of turtle population decline. However, empirical evidence of the direct negative effects of road mortality on turtle population abundance is lacking. The purpose of this study was to provide a strong test of the prediction that roads reduce turtle population abundance. While controlling for potentially confounding variables, we compared relative abundance of painted turtles (Chrysemys picta) in 20 ponds in Eastern Ontario, 10 as close as possible to high traffic roads (Road sites) and 10 as far as possible from any major roads (No Road sites). There was no significant effect of roads on painted turtle relative abundance. Furthermore, our data do not support other predictions of the road mortality hypothesis; we observed neither a higher relative frequency of males to females at Road sites than at No Road sites, nor a lower average body size of turtles at Road than at No Road sites. We speculate that, although roads can cause substantial adult mortality in turtles, other factors, such as release from predation on adults and/or nests close to roads counter the negative effect of road mortality in some populations. We suggest that road mitigation for painted turtles can be limited to locations where turtles are forced to migrate across high traffic roads due, for example, to destruction of local nesting habitat or seasonal drying of ponds. This conclusion should not be extrapolated to other species of turtles, where road mortality could have a larger population-level effect than on painted turtles.     

AutoDecon, a deconvolution algorithm for identification and characterization of luteinizing hormone secretory bursts: description and validation using synthetic data

Hormone signaling is often pulsatile, and multiparameter deconvolution procedures have long been used to identify and characterize secretory events. However, the existing programs have serious limitations, including the subjective nature of initial peak selection, lack of statistical verification of presumed bursts, and user-unfriendliness of the application. Here we describe a novel deconvolution program, AutoDecon, which addresses these concerns. We validate AutoDecon for application to serum luteinizing hormone (LH) concentration time series using synthetic data mimicking real data from normal women and then comparing the performance of AutoDecon with the performance of the widely employed hormone pulsatility analysis program Cluster. The sensitivity of AutoDecon is higher than that of Cluster (∼ 96% vs. 80%, P = 0.001). However, Cluster had a lower false-positive detection rate than did AutoDecon (6% vs. 1%, P = 0.001). Further analysis demonstrated that the pulsatility parameters recovered by AutoDecon were indistinguishable from those characterizing the synthetic data and that sampling at 5- or 10-min intervals was optimal for maximizing the sensitivity rates for LH. Accordingly, AutoDecon presents a viable nonsubjective alternative to previous pulse detection algorithms for the analysis of LH data. It is applicable to other pulsatile hormone concentration time series and many other pulsatile phenomena. The software is free and downloadable at http://mljohnson.pharm.virginia.edu/home.html.     

Matt: local flexibility aids protein multiple structure alignment

Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these “bent” alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of α-helices and β-strands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse protein-folding problem. The related question of whether Matt alignments can be used to distinguish distantly homologous structure pairs from pairs of proteins that are not homologous is also considered. For this purpose, a p-value score based on the length of the common core and average root mean squared deviation (RMSD) of Matt alignments is shown to largely separate decoys from homologous protein structures in the SABmark benchmark dataset. We postulate that Matt's strong performance comes from its ability to model proteins in different conformational states and, perhaps even more important, its ability to model backbone distortions in more distantly related proteins.