Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination

Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by ϕC31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. ϕC31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition

Stochastic background of gravitational waves

A continuous stochastic background of gravitational waves (GWs) for burst sources is produced if the mean time interval between the occurrence of bursts is smaller than the average time duration of a single burst at the emission, i.e., the so called duty cycle must be greater than one. To evaluate the background of GWs produced by an ensemble of sources, during their formation, for example, one needs to know the average energy flux emitted during the formation of a single object and the formation rate of such objects as well. In many cases the energy flux emitted during an event of production of GWs is not known in detail, only characteristic values for the dimensionless amplitude and frequencies are known. Here we present a shortcut to calculate stochastic backgrounds of GWs produced from cosmological sources. For this approach it is not necessary to know in detail the energy flux emitted at each frequency. Knowing the characteristic values for the ``lumped'' dimensionless amplitude and frequency we show that it is possible to calculate the stochastic background of GWs produced by an ensemble of sources.Comment: 6 pages, 4 eps figures, (Revtex) Latex. Physical Review D (in press

Efficient base driver circuit for silicon carbide bipolar junction transistors

The silicon carbide bipolar junction transistor needs large transient currents supplied into and out of its base terminal for rapid switching. To realise this, it is normally desirable to have a base driver circuit supply rail at a high voltage. However, the device also needs a steady base current to hold it in the on-state. Supplying this current from a highvoltage source is inefficient. A circuit is presented that applies high transient base-emitter voltages, but with low driver circuit power consumption

An approximate renormalization-group transformation for Hamiltonian systems with three degrees of freedom

We construct an approximate renormalization transformation that combines Kolmogorov-Arnold-Moser (KAM)and renormalization-group techniques, to analyze instabilities in Hamiltonian systems with three degrees of freedom. This scheme is implemented both for isoenergetically nondegenerate and for degenerate Hamiltonians. For the spiral mean frequency vector, we find numerically that the iterations of the transformation on nondegenerate Hamiltonians tend to degenerate ones on the critical surface. As a consequence, isoenergetically degenerate and nondegenerate Hamiltonians belong to the same universality class, and thus the corresponding critical invariant tori have the same type of scaling properties. We numerically investigate the structure of the attracting set on the critical surface and find that it is a strange nonchaotic attractor. We compute exponents that characterize its universality class.Comment: 10 pages typeset using REVTeX, 7 PS figure

The baryonic collapse efficiency of galaxy groups in the RESOLVE and ECO surveys

We examine the z = 0 group-integrated stellar and cold baryonic (stars + cold atomic gas) mass functions (group SMF and CBMF) and the baryonic collapse efficiency (group cold baryonic to dark matter halo mass ratio) using the RESOLVE and ECO survey galaxy group catalogs and a GALFORM semi-analytic model (SAM) mock catalog. The group SMF and CBMF fall off more steeply at high masses and rise with a shallower low-mass slope than the theoretical halo mass function (HMF). The transition occurs at the group-integrated cold baryonic mass Mbary cold ~ 1011 M. The SAM, however, has significantly fewer groups at the transition mass ∼1011 M and a steeper low-mass slope than the data, suggesting that feedback is too weak in low-mass halos and conversely too strong near the transition mass. Using literature prescriptions to include hot halo gas and potential unobservable galaxy gas produces a group BMF with a slope similar to the HMF even below the transition mass. Its normalization is lower by a factor of ∼2, in agreement with estimates of warm-hot gas making up the remaining difference. We compute baryonic collapse efficiency with the halo mass calculated two ways, via halo abundance matching (HAM) and via dynamics (extended all the way to three-galaxy groups using stacking). Using HAM, we find that baryonic collapse efficiencies reach a flat maximum for groups across the halo mass range of Mhalo ~ 1011.4 - 12 M, which we label “nascent groups.” Using dynamics, however, we find greater scatter in baryonic collapse efficiencies, likely indicating variation in group hot-to-cold baryon ratios. Similarly, we see higher scatter in baryonic collapse efficiencies in the SAM when using its true groups and their group halo masses as opposed to friends-of-friends groups and HAM masses

Void galaxies follow a distinct evolutionary path in the environmental context catalog

We measure the environmental dependence, where environment is defined by the distance to the third nearest neighbor, of multiple galaxy properties inside the Environmental COntext (ECO) catalog. We focus primarily on void galaxies, which we define as the 10% of galaxies having the lowest local density. We compare the properties of void and non-void galaxies: baryonic mass, color, fractional stellar mass growth rate (FSMGR), morphology, and gas-to-stellar-mass ratio (estimated from a combination of H I data and photometric gas fractions calibrated with the REsolved Spectroscopy Of a Local VolumE survey). Our void galaxies typically have lower baryonic masses than galaxies in denser environments, and they display the properties expected of a lower mass population: they have more late types, are bluer, have a higher FSMGR, and are more gas-rich. We control for baryonic mass and investigate the extent to which void galaxies are different at fixed mass. Void galaxies are bluer, more gas-rich, and more star-forming at fixed mass than non-void galaxies, which is a possible signature of galaxy assembly bias. Furthermore, we show that these trends persist even at fixed mass and morphology, and we find that voids host a distinct population of early types that are bluer and more star-forming than the typical red and quenched early types. In addition to these empirical observational results, we also present theoretical results from mock catalogs with built-in galaxy assembly bias. We show that a simple matching of galaxy properties to (sub)halo properties, such as mass and age, can recover the observed environmental trends in ECO galaxies

Primordialists and Constructionists: a typology of theories of religion

This article adopts categories from nationalism theory to classify theories of religion. Primordialist explanations are grounded in evolutionary psychology and emphasize the innate human demand for religion. Primordialists predict that religion does not decline in the modern era but will endure in perpetuity. Constructionist theories argue that religious demand is a human construct. Modernity initially energizes religion, but subsequently undermines it. Unpacking these ideal types is necessary in order to describe actual theorists of religion. Three distinctions within primordialism and constructionism are relevant. Namely those distinguishing: a) materialist from symbolist forms of constructionism; b) theories of origins from those pertaining to the reproduction of religion; and c) within reproduction, between theories of religious persistence and secularization. This typology helps to make sense of theories of religion by classifying them on the basis of their causal mechanisms, chronology and effects. In so doing, it opens up new sightlines for theory and research

Debris disk size distributions: steady state collisional evolution with P-R drag and other loss processes

We present a new scheme for determining the shape of the size distribution, and its evolution, for collisional cascades of planetesimals undergoing destructive collisions and loss processes like Poynting-Robertson drag. The scheme treats the steady state portion of the cascade by equating mass loss and gain in each size bin; the smallest particles are expected to reach steady state on their collision timescale, while larger particles retain their primordial distribution. For collision-dominated disks, steady state means that mass loss rates in logarithmic size bins are independent of size. This prescription reproduces the expected two phase size distribution, with ripples above the blow-out size, and above the transition to gravity-dominated planetesimal strength. The scheme also reproduces the expected evolution of disk mass, and of dust mass, but is computationally much faster than evolving distributions forward in time. For low-mass disks, P-R drag causes a turnover at small sizes to a size distribution that is set by the redistribution function (the mass distribution of fragments produced in collisions). Thus information about the redistribution function may be recovered by measuring the size distribution of particles undergoing loss by P-R drag, such as that traced by particles accreted onto Earth. Although cross-sectional area drops with 1/age^2 in the PR-dominated regime, dust mass falls as 1/age^2.8, underlining the importance of understanding which particle sizes contribute to an observation when considering how disk detectability evolves. Other loss processes are readily incorporated; we also discuss generalised power law loss rates, dynamical depletion, realistic radiation forces and stellar wind drag.Comment: Accepted for publication by Celestial Mechanics and Dynamical Astronomy (special issue on EXOPLANETS

Measurement of the p-pbar -> Wgamma + X cross section at sqrt(s) = 1.96 TeV and WWgamma anomalous coupling limits

The WWgamma triple gauge boson coupling parameters are studied using p-pbar -> l nu gamma + X (l = e,mu) events at sqrt(s) = 1.96 TeV. The data were collected with the DO detector from an integrated luminosity of 162 pb^{-1} delivered by the Fermilab Tevatron Collider. The cross section times branching fraction for p-pbar -> W(gamma) + X -> l nu gamma + X with E_T^{gamma} > 8 GeV and Delta R_{l gamma} > 0.7 is 14.8 +/- 1.6 (stat) +/- 1.0 (syst) +/- 1.0 (lum) pb. The one-dimensional 95% confidence level limits on anomalous couplings are -0.88 < Delta kappa_{gamma} < 0.96 and -0.20 < lambda_{gamma} < 0.20.Comment: Submitted to Phys. Rev. D Rapid Communication

Measurement of the ttbar Production Cross Section in ppbar Collisions at sqrt{s} = 1.96 TeV using Kinematic Characteristics of Lepton + Jets Events

We present a measurement of the top quark pair ttbar production cross section in ppbar collisions at a center-of-mass energy of 1.96 TeV using 230 pb**{-1} of data collected by the DO detector at the Fermilab Tevatron Collider. We select events with one charged lepton (electron or muon), large missing transverse energy, and at least four jets, and extract the ttbar content of the sample based on the kinematic characteristics of the events. For a top quark mass of 175 GeV, we measure sigma(ttbar) = 6.7 {+1.4-1.3} (stat) {+1.6- 1.1} (syst) +/-0.4 (lumi) pb, in good agreement with the standard model prediction.Comment: submitted to Phys.Rev.Let