Accretion onto the Companion of Eta Carinae During the Spectroscopic Event: II. X-Ray Emission Cycle

We calculate the X-ray luminosity and light curve for the stellar binary system Eta Carinae for the entire orbital period of 5.54 years. By using a new approach we find, as suggested before, that the collision of the winds blown by the two stars can explain the X-ray emission and temporal behavior. Most X-ray emission in the 2-10 \kev band results from the shocked secondary stellar wind. The observed rise in X-ray luminosity just before minimum is due to increase in density and subsequent decrease in radiative cooling time of the shocked fast secondary wind. Absorption, particularly of the soft X-rays from the primary wind, increases as the system approaches periastron and the shocks are produced deep inside the primary wind. However, absorption can not account for the drastic X-ray minimum. The 70 day minimum is assumed to result from the collapse of the collision region of the two winds onto the secondary star. This process is assumed to shut down the secondary wind, hence the main X-ray source. We show that this assumption provides a phenomenological description of the X-ray behavior around the minimum.Comment: The Astrophysical Journal, in pres

Why highly expressed proteins evolve slowly

Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons which have remained unexplained. Here, we hypothesize that selection to reduce the burden of protein misfolding will favor protein sequences with increased robustness to translational missense errors. Pressure for translational robustness increases with expression level and constrains sequence evolution. Using several sequenced yeast genomes, global expression and protein abundance data, and sets of paralogs traceable to an ancient whole-genome duplication in yeast, we rule out several confounding effects and show that expression level explains roughly half the variation in Saccharomyces cerevisiae protein evolutionary rates. We examine causes for expression's dominant role and find that genome-wide tests favor the translational robustness explanation over existing hypotheses that invoke constraints on function or translational efficiency. Our results suggest that proteins evolve at rates largely unrelated to their functions, and can explain why highly expressed proteins evolve slowly across the tree of life.Comment: 40 pages, 3 figures, with supporting informatio

Universality of weak selection

Weak selection, which means a phenotype is slightly advantageous over another, is an important limiting case in evolutionary biology. Recently it has been introduced into evolutionary game theory. In evolutionary game dynamics, the probability to be imitated or to reproduce depends on the performance in a game. The influence of the game on the stochastic dynamics in finite populations is governed by the intensity of selection. In many models of both unstructured and structured populations, a key assumption allowing analytical calculations is weak selection, which means that all individuals perform approximately equally well. In the weak selection limit many different microscopic evolutionary models have the same or similar properties. How universal is weak selection for those microscopic evolutionary processes? We answer this question by investigating the fixation probability and the average fixation time not only up to linear, but also up to higher orders in selection intensity. We find universal higher order expansions, which allow a rescaling of the selection intensity. With this, we can identify specific models which violate (linear) weak selection results, such as the one--third rule of coordination games in finite but large populations.Comment: 12 pages, 3 figures, accepted for publication in Physical Review

Amplified biochemical oscillations in cellular systems

We describe a mechanism for pronounced biochemical oscillations, relevant to microscopic systems, such as the intracellular environment. This mechanism operates for reaction schemes which, when modeled using deterministic rate equations, fail to exhibit oscillations for any values of rate constants. The mechanism relies on amplification of the underlying stochasticity of reaction kinetics within a narrow window of frequencies. This amplification allows fluctuations to beat the central limit theorem, having a dominant effect even though the number of molecules in the system is relatively large. The mechanism is quantitatively studied within simple models of self-regulatory gene expression, and glycolytic oscillations.Comment: 35 pages, 6 figure

Genome landscapes and bacteriophage codon usage

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E. coli, P. aeruginosa and L. lactis as their primary host. We introduce the concept of a `genome landscape,' which helps reveal non-trivial, long-range patterns in codon usage across a genome. We develop a series of randomization tests that allow us to interrogate the significance of one aspect of codon usage, such a GC content, while controlling for another aspect, such as adaptation to host-preferred codons. We find that 33 phage genomes exhibit highly non-random patterns in their GC3-content, use of host-preferred codons, or both. We show that the head and tail proteins of these phages exhibit significant bias towards host-preferred codons, relative to the non-structural phage proteins. Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages.Comment: 9 Color Figures, 5 Tables, 53 Reference

CD20 and CD19 targeted vectors induce minimal activation of resting B lymphocytes

B lymphocytes are an important cell population of the immune system. However, until recently it was not possible to transduce resting B lymphocytes with retro- or lentiviral vectors, making them unsusceptible for genetic manipulations by these vectors. Lately, we demonstrated that lentiviral vectors pseudotyped with modified measles virus (MV) glycoproteins hemagglutinin, responsible for receptor recognition, and fusion protein were able to overcome this transduction block. They use either the natural MV receptors, CD46 and signaling lymphocyte activation molecule (SLAM), for cell entry (MV-LV) or the vector particles were further modified to selectively enter via the CD20 molecule, which is exclusively expressed on B lymphocytes (CD20-LV). It has been shown previously that transduction by MV-LV does not induce B lymphocyte activation. However, if this is also true for CD20-LV is still unknown. Here, we generated a vector specific for another B lymphocyte marker, CD19, and compared its ability to transduce resting B lymphocytes with CD20-LV. The vector (CD19ds-LV) was able to stably transduce unstimulated B lymphocytes, albeit with a reduced efficiency of about 10% compared to CD20-LV, which transduced about 30% of the cells. Since CD20 as well as CD19 are closely linked to the B lymphocyte activation pathway, we investigated if engagement of CD20 or CD19 molecules by the vector particles induces activating stimuli in resting B lymphocytes. Although, activation of B lymphocytes often involves calcium influx, we did not detect elevated calcium levels. However, the activation marker CD71 was substantially up-regulated upon CD20-LV transduction and most importantly, B lymphocytes transduced with CD20-LV or CD19ds-LV entered the G1b phase of cell cycle, whereas untransduced or MV-LV transduced B lymphocytes remained in G0. Hence, CD20 and CD19 targeting vectors induce activating stimuli in resting B lymphocytes, which most likely renders them susceptible for lentiviral vector transduction

From Bipolar to Elliptical: Simulating the Morphological Evolution of Planetary Nebulae

The majority of Proto-planetary nebulae (PPN) are observed to have bipolar morphologies. The majority of mature PN are observed to have elliptical shapes. In this paper we address the evolution of PPN/PN morphologies attempting to understand if a transition from strongly bipolar to elliptical shape can be driven by changes in the parameters of the mass loss process. To this end we present 2.5D hydrodynamical simulations of mass loss at the end stages of stellar evolution for intermediate mass stars. We track changes in wind velocity, mass loss rate and mass loss geometry. In particular we focus on the transition from mass loss dominated by a short duration jet flow (driven during the PPN phase) to mass loss driven by a spherical fast wind (produced by the central star of the PN). We address how such changes in outflow characteristics can change the nebula from a bipolar to an elliptical morphology. Our results show that including a period of jet formation in the temporal sequence of PPN to PN produces realistic nebular synthetic emission geometries. More importantly such a sequence provides insight, in principle, into the apparent difference in morphology statistics characterizing PPN and PN systems. In particular we find that while jet driven PPN can be expected to be dominated by bipolar morphologies, systems that begin with a jet but are followed by a spherical fast wind will evolve into elliptical nebulae. Furthermore, we find that spherical nebulae are highly unlikely to ever derive from either bipolar PPN or elliptical PN.Comment: Accepted for publication in the MNRAS, 15 pages, 7 figure

The Majorana Project

Building a \BBz experiment with the ability to probe neutrino mass in the inverted hierarchy region requires the combination of a large detector mass sensitive to \BBz, on the order of 1-tonne, and unprecedented background levels, on the order of or less than 1 count per year in the \BBz signal region. The MAJORANA Collaboration proposes a design based on using high-purity enriched Ge-76 crystals deployed in ultra-low background electroformed Cu cryostats and using modern analysis techniques that should be capable of reaching the required sensitivity while also being scalable to a 1-tonne size. To demonstrate feasibility, the collaboration plans to construct a prototype system, the MAJORANA DEMONSTRATOR, consisting of 30 kg of 86% enriched \Ge-76 detectors and 30 kg of natural or isotope-76-depleted Ge detectors. We plan to deploy and evaluate two different Ge detector technologies, one based on a p-type configuration and the other on n-type.Comment: paper submitted for the 2008 Carolina International Symposium on Neutrino Physic

Time resolved spectroscopy of BD+46 442: gas streams and jet creation in a newly discovered evolved binary with a disk

Previous studies have shown that many post-AGB stars with dusty disks are associated with single-lined binary stars. To verify the binarity hypothesis on a larger sample, we started a high-resolution spectral monitoring of about 40 field giants, whose binarity was suspected based on either a light curve, an infrared excess, or a peculiar chemical composition. Here we report on the discovery of the periodic RV variations in BD+46 442, a high-latitude F giant with a disk. We interpret the variations due to the motion around a faint companion, and deduce the following orbital parameters: Porb = 140.77 d, e = 0.083, asini=0.31 AU. We find it to be a moderately metal-poor star ([M/H]=-0.7) without a strong depletion pattern in the photospheric abundances. Interestingly, many lines show periodic changes with the orbital phase: Halpha switches between a double-peak emission and a PCyg-like profiles, while strong metal lines appear split during the maximum redshift. Similar effects are likely visible in the spectra of other post-AGB binaries, but their regularity is not always realized due to sporadic observations. We propose that these features result from an ongoing mass transfer from the evolved giant to the companion. In particular, the blue-shifted absorption in Halpha, which occurs only at superior conjunction, may result from a jet originating in the accretion disk around the companion and seen in absorption towards the luminous primary.Comment: 16 pages, accepted in A&

Inferring stabilizing mutations from protein phylogenies : application to influenza hemagglutinin

One selection pressure shaping sequence evolution is the requirement that a protein fold with sufficient stability to perform its biological functions. We present a conceptual framework that explains how this requirement causes the probability that a particular amino acid mutation is fixed during evolution to depend on its effect on protein stability. We mathematically formalize this framework to develop a Bayesian approach for inferring the stability effects of individual mutations from homologous protein sequences of known phylogeny. This approach is able to predict published experimentally measured mutational stability effects (ΔΔG values) with an accuracy that exceeds both a state-of-the-art physicochemical modeling program and the sequence-based consensus approach. As a further test, we use our phylogenetic inference approach to predict stabilizing mutations to influenza hemagglutinin. We introduce these mutations into a temperature-sensitive influenza virus with a defect in its hemagglutinin gene and experimentally demonstrate that some of the mutations allow the virus to grow at higher temperatures. Our work therefore describes a powerful new approach for predicting stabilizing mutations that can be successfully applied even to large, complex proteins such as hemagglutinin. This approach also makes a mathematical link between phylogenetics and experimentally measurable protein properties, potentially paving the way for more accurate analyses of molecular evolution