Spatial Dynamics of Alternative Reproductive Strategies: The Role of Nieghbors

In territorial species, the reproductive success of a male is dependent on the quality of his territory. One important component of territory quality is spatial location. High-quality territories not only should be located in areas of high food abundance and low predation, but also should be located in areas that offer optimal amounts of social interaction. Such optima might be different for individuals according to their sex, dominance, or genotype. We studied territory quality (size, vegetation structure, and placement) in a socially monogamous, polymorphic passerine, the White-throated Sparrow (Zonotrichia albicollis), in order to determine how spatial attributes contribute to selection intensity on two genotypes. In this species, plumage (white and tan), behavior, and life-history characteristics have a genetic basis and are correlated with the presence or absence of a chromosomal inversion. Using remote sensing and Geographic Information Systems (GIS), we found that the territories of white and tan males do not differ in size or vegetation structure, suggesting that these factors are not of primary importance to males when deciding where to establish a territory. Instead, we suggest that the placement of white and tan territories depends on the number of neighbors (particularly, white male neighbors). Tan males settle in low-density, neighbor-restrictive habitats where intruder pressure from white males seeking extra-pair copulations is reduced. In contrast, white males tend to settle in high-density areas where the probability of encountering neighboring fertile females is greatest. This segregation has led to intraspecific niche partitioning in the two disassortative pair types so that each male morph can best exploit its respective reproductive strategies. These factors may, in turn, contribute to the maintenance of this unusual mating system and, ultimately, the stability of the polymorphism in this species. Similar forces may be operating in other species without distinct morphological markers; we suggest that researchers keep social factors in mind when examining habitat selection

Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments

It has long been proposed that much of the information encoding how a protein folds is contained locally in the peptide chain. Here we present a large-scale simulation study designed to examine the extent to which conformations of peptide fragments in water predict native conformations in proteins. We perform replica exchange molecular dynamics (REMD) simulations of 872 8-mer, 12-mer, and 16-mer peptide fragments from 13 proteins using the AMBER 96 force field and the OBC implicit solvent model. To analyze the simulations, we compute various contact-based metrics, such as contact probability, and then apply Bayesian classifier methods to infer which metastable contacts are likely to be native vs. non-native. We find that a simple measure, the observed contact probability, is largely more predictive of a peptide's native structure in the protein than combinations of metrics or multi-body components. Our best classification model is a logistic regression model that can achieve up to 63% correct classifications for 8-mers, 71% for 12-mers, and 76% for 16-mers. We validate these results on fragments of a protein outside our training set. We conclude that local structure provides information to solve some but not all of the conformational search problem. These results help improve our understanding of folding mechanisms, and have implications for improving physics-based conformational sampling and structure prediction using all-atom molecular simulations

Cover slip external cavity diode laser

The design of a 671 nm diode laser with a mode-hop-free tuning range of 40 GHz is described. This long tuning range is achieved by simultaneously ramping the external cavity length with the laser injection current. The external cavity consists of a microscope cover slip mounted on piezoelectric actuators. In such a configuration the laser output pointing remains fixed, independent of its frequency. Using a diode with an output power of 5-7 mW, the laser linewidth was found to be smaller than 30 MHz. This cover slip cavity and feedforward laser current control system is simple, economical, robust, and easy to use for spectroscopy, as we demonstrate with lithium vapor and lithium atom beam experiments.Comment: 7 pages, 6 figures, submitted to Review of Scientific Instruments 7/29/0

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics.

As sequencing read length has increased, researchers have quickly adopted longer reads for their experiments. Here, we examine 14 pathogen or host-pathogen differential gene expression data sets to assess whether using longer reads is warranted. A variety of data sets was used to assess what genomic attributes might affect the outcome of differential gene expression analysis including: gene density, operons, gene length, number of introns/exons and intron length. No genome attribute was found to influence the data in principal components analysis, hierarchical clustering with bootstrap support, or regression analyses of pairwise comparisons that were undertaken on the same reads, looking at all combinations of paired and unpaired reads trimmed to 36, 54, 72 and 101 bp. Read pairing had the greatest effect when there was little variation in the samples from different conditions or in their replicates (e.g. little differential gene expression). But overall, 54 and 72 bp reads were typically most similar. Given differences in costs and mapping percentages, we recommend 54 bp reads for organisms with no or few introns and 72 bp reads for all others. In a third of the data sets, read pairing had absolutely no effect, despite paired reads having twice as much data. Therefore, single-end reads seem robust for differential-expression analyses, but in eukaryotes paired-end reads are likely desired to analyse splice variants and should be preferred for data sets that are acquired with the intent to be community resources that might be used in secondary data analyses

SpECTRE: A Task-based Discontinuous Galerkin Code for Relativistic Astrophysics

We introduce a new relativistic astrophysics code, SpECTRE, that combines a discontinuous Galerkin method with a task-based parallelism model. SpECTRE's goal is to achieve more accurate solutions for challenging relativistic astrophysics problems such as core-collapse supernovae and binary neutron star mergers. The robustness of the discontinuous Galerkin method allows for the use of high-resolution shock capturing methods in regions where (relativistic) shocks are found, while exploiting high-order accuracy in smooth regions. A task-based parallelism model allows efficient use of the largest supercomputers for problems with a heterogeneous workload over disparate spatial and temporal scales. We argue that the locality and algorithmic structure of discontinuous Galerkin methods will exhibit good scalability within a task-based parallelism framework. We demonstrate the code on a wide variety of challenging benchmark problems in (non)-relativistic (magneto)-hydrodynamics. We demonstrate the code's scalability including its strong scaling on the NCSA Blue Waters supercomputer up to the machine's full capacity of 22,380 nodes using 671,400 threads.Comment: 41 pages, 13 figures, and 7 tables. Ancillary data contains simulation input file

Helix 11 Dynamics Is Critical for Constitutive Androstane Receptor Activity

SummaryThe constitutive androstane receptor (CAR) transactivation can occur in the absence of exogenous ligand and this activity is enhanced by agonists TCPOBOP and meclizine. We use biophysical and cell-based assays to show that increased activity of CAR(TCPOBOP) relative to CAR(meclizine) corresponds to a higher affinity of CAR(TCPOBOP) for the steroid receptor coactivator-1. Additionally, steady-state fluorescence spectra suggest conformational differences between CAR(TCPOBOP):RXR and CAR(meclizine):RXR. Hydrogen/deuterium exchange (HDX) data indicate that the CAR activation function 2 (AF-2) is more stable in CAR(TCPOBOP):RXR and CAR(meclizine):RXR than in CAR:RXR. HDX kinetics also show significant differences between CAR(TCPOBOP):RXR and CAR(meclizine):RXR. Unlike CAR(meclizine):RXR, CAR(TCPOBOP):RXR shows a higher overall stabilization that extends into RXR. We identify residues 339–345 in CAR as an allosteric regulatory site with a greater magnitude reduction in exchange kinetics in CAR(TCPOBOP):RXR than CAR(meclizine):RXR. Accordingly, assays with mutations on CAR at leucine-340 and leucine-343 confirm this region as an important determinant of CAR activity

Behavioral and physiological responses to male handicap in chick-rearing black-legged kittiwakes

Parental investment entails a trade-off between the benefits of effort in current offspring and the costs to future reproduction. Long-lived species are predicted to be reluctant to increase parental effort to avoid affecting their survival. We tested this hypothesis in black-legged kittiwakes Rissa tridactyla by clipping flight feathers of experimental males at the beginning of the chick-rearing period. We analyzed the consequences of this handicap on feeding and attendance behavior, body condition, integument coloration, and circulating levels of corticosterone and prolactin in handicapped males and their mates in comparison to unmanipulated controls. Chicks in both groups were compared in terms of aggressive behavior, growth, and mortality. Handicapped males lost more mass, had less bright integuments, and attended the nest less often than controls. Nevertheless, they fed their chicks at the same rate and had similar corticosterone and prolactin levels. Compared with control females, females mated with handicapped males showed a lower provisioning rate and higher nest attendance in the first days after manipulation. Their lower feeding rate probably triggered the increased sibling aggression and mortality observed in experimental broods. Our findings suggest that experimental females adaptively adjusted their effort to their mate's perceived quality or that their provisioning was constrained by their higher nest attendance. Overall, our results suggest that kittiwake males can decrease their condition for the sake of their chicks, which seems to contradict the hypothesis that kittiwakes should be reluctant to increase parental effort to avoid affecting their surviva

Influence of Xpand Nitric Oxide Reactor, L-Arginine Alpha-Ketoglutarate, and Caffeine Supplementation on Calf Muscle Re-Oxygenation During and after Acute Resistance Exercise

Xpand Nitric Oxide Reactor is a "cocktail" supplement proposed to improve skeletal muscle blood flow via arginine's effect on nitric oxide synthesis and vasodilation. Two other major ingredients, caffeine and creatine, cause vasoconstriction, which could potentially counteract the proposed hemodynamic effects of arginine. The purpose of this study was to examine the influence of Xpand Nitric Oxide Reactor on muscle re-oxygenation after resistance exercise compared to supplementation with constituent ingredients L-arginine alpha-ketoglutarate and caffeine. Nine recreationally active men (21±1y) performed 3 sets of 20 repetitions of seated single-leg calf raise at 60% 1-RM with 3 min rests. The same calf raise exercise was performed following 4 separate supplementation conditions: L-arginine alpha-ketoglutarate (AAKG), caffeine (CAFF), Xpand Nitric Oxide Reactor (XPAND), and placebo (PLAC). Soleus muscle re-oxygenation time was measured before, during, and immediately after exercise using near infrared spectroscopy. Supplementation with XPAND (0.43±0.03), AAKG (0.34±0.02), and CAFF (0.45±0.05) did not significantly affect muscle re-oxygenation halftime (minutes) compared to placebo (0.35±0.04). An arginine containing "cocktail" supplement did not affect skeletal muscle re-oxygenation after resistance exercise, possibly due to a wash-out effect caused by the multiple ingredients