The pause-initiation limit restricts transcription activation in human cells.

Eukaryotic gene transcription is often controlled at the level of RNA polymerase II (Pol II) pausing in the promoter-proximal region. Pausing Pol II limits the frequency of transcription initiation ('pause-initiation limit'), predicting that the pause duration must be decreased for transcriptional activation. To test this prediction, we conduct a genome-wide kinetic analysis of the heat shock response in human cells. We show that the pause-initiation limit restricts transcriptional activation at most genes. Gene activation generally requires the activity of the P-TEFb kinase CDK9, which decreases the duration of Pol II pausing and thereby enables an increase in the productive initiation frequency. The transcription of enhancer elements is generally not pause limited and can be activated without CDK9 activity. Our results define the kinetics of Pol II transcriptional regulation in human cells at all gene classes during a natural transcription response

New scaling for the alpha effect in slowly rotating turbulence

Using simulations of slowly rotating stratified turbulence, we show that the alpha effect responsible for the generation of astrophysical magnetic fields is proportional to the logarithmic gradient of kinetic energy density rather than that of momentum, as was previously thought. This result is in agreement with a new analytic theory developed in this paper for large Reynolds numbers. Thus, the contribution of density stratification is less important than that of turbulent velocity. The alpha effect and other turbulent transport coefficients are determined by means of the test-field method. In addition to forced turbulence, we also investigate supernova-driven turbulence and stellar convection. In some cases (intermediate rotation rate for forced turbulence, convection with intermediate temperature stratification, and supernova-driven turbulence) we find that the contribution of density stratification might be even less important than suggested by the analytic theory.Comment: 10 pages, 9 figures, revised version, Astrophys. J., in pres

Probing the Protosolar Disk Using Dust Filtering at Gaps in the Early Solar System

Jupiter and Saturn formed early, before the gas disk dispersed. The presence of gap-opening planets affects the dynamics of the gas and embedded solids and halts the inward drift of grains above a certain size. A drift barrier can explain the absence of calcium aluminium rich inclusions (CAIs) in chondrites originating from parent bodies that accreted in the inner solar system. Employing an interdisciplinary approach, we use a $\mu$-X-Ray-fluorescence scanner to search for large CAIs and a scanning electron microscope to search for small CAIs in the ordinary chondrite NWA 5697. We carry out long-term, two-dimensional simulations including gas, dust, and planets to characterize the transport of grains within the viscous $\alpha$-disk framework exploring the scenarios of a stand-alone Jupiter, Jupiter and Saturn \textit{in situ}, or Jupiter and Saturn in a 3:2 resonance. In each case, we find a critical grain size above which drift is halted as a function of the physical conditions in the disk. From the laboratory search we find four CAIs with a largest size of $\approx$200$\,\mu$m. \Combining models and data, we provide an estimate for the upper limit of the $\alpha$-viscosity and the surface density at the location of Jupiter, using reasonable assumptions about the stellar accretion rate during inward transport of CAIs, and assuming angular momentum transport to happen exclusively through viscous effects. Moreover, we find that the compound gap structure in the presence of Saturn in a 3:2 resonance favors inward transport of grains larger than CAIs currently detected in ordinary chondrites.Comment: 16 pages, 10 figures, updated to match published version in Astrophysical Journa

Low-mass planet migration in three-dimensional wind-driven inviscid discs: a negative corotation torque

We present simulations of low-mass planet–disc interactions in inviscid three-dimensional discs. We show that a wind-driven laminar accretion flow through the surface layers of the disc does not significantly modify the migration torque experienced by embedded planets. More importantly, we find that 3D effects lead to a dramatic change in the behaviour of the dynamical corotation torque compared to earlier 2D theory and simulations. Although it was previously shown that the dynamical corotation torque could act to slow and essentially stall the inward migration of a low-mass planet, our results in 3D show that the dynamical corotation torque has the complete opposite effect and speeds up inward migration. Our numerical experiments implicate buoyancy resonances as the cause. These have two effects: (i) they exert a direct torque on the planet, whose magnitude relative to the Lindblad torque is measured in our simulations to be small; (ii) they torque the gas librating on horseshoe orbits in the corotation region and drive evolution of its vortensity, leading to the negative dynamical corotation torque. This indicates that at low turbulent viscosity, the detailed vertical thermal structure of the protoplanetary disc plays an important role in determining the migration behaviour of embedded planets. If this result holds up under a more refined treatment of disc thermal evolution, then it has important implications for understanding the formation and early evolution of planetary systems

Global bifurcations to subcritical magnetorotational dynamo action in Keplerian shear flow

Magnetorotational dynamo action in Keplerian shear flow is a three-dimensional, non-linear magnetohydrodynamic process whose study is relevant to the understanding of accretion processes and magnetic field generation in astrophysics. Transition to this form of dynamo action is subcritical and shares many characteristics of transition to turbulence in non-rotating hydrodynamic shear flows. This suggests that these different fluid systems become active through similar generic bifurcation mechanisms, which in both cases have eluded detailed understanding so far. In this paper, we build on recent work on the two problems to investigate numerically the bifurcation mechanisms at work in the incompressible Keplerian magnetorotational dynamo problem in the shearing box framework. Using numerical techniques imported from dynamical systems research, we show that the onset of chaotic dynamo action at magnetic Prandtl numbers larger than unity is primarily associated with global homoclinic and heteroclinic bifurcations of nonlinear magnetorotational dynamo cycles. These global bifurcations are found to be supplemented by local bifurcations of cycles marking the beginning of period-doubling cascades. The results suggest that nonlinear magnetorotational dynamo cycles provide the pathway to turbulent injection of both kinetic and magnetic energy in incompressible magnetohydrodynamic Keplerian shear flow in the absence of an externally imposed magnetic field. Studying the nonlinear physics and bifurcations of these cycles in different regimes and configurations may subsequently help to better understand the physical conditions of excitation of magnetohydrodynamic turbulence and instability-driven dynamos in a variety of astrophysical systems and laboratory experiments. The detailed characterization of global bifurcations provided for this three-dimensional subcritical fluid dynamics problem may also prove useful for the problem of transition to turbulence in hydrodynamic shear flows

GM crops and gender issues

Correspondence in the December issue by Jonathan Gressel not only states that gender issues in rural settings have not been adequately addressed with respect to weed control biotech but also asserts that such technology can increase the quality of life of rural women in developing countries. Improved weed control is a labor-saving technology that can result in less employment in a labor surplus rural economy. Often in rural areas, wage income is the main source of income and an important determinant of the quality of life, particularly where employment opportunities are generally limited. Apart from soil preparation, planting and weeding, harvesting is also 'femanual' work that can generate more employment if yields are higher. Biotech can enhance the quality of life of women but only if the technology is associated with overall generation of rural employment

On the dynamics of planetesimals embedded in turbulent protoplanetary discs with dead zones

(abridged) Accretion in protoplanetary discs is thought to be driven by [...] turbulence via the magnetorotational instability (MRI). Recent work has shown that a planetesimal swarm embedded in a fully turbulent disc is subject to strong excitation of the velocity dispersion, leading to collisional destruction of bodies with radii R_p < 100 km. Significant diffusion of planetesimal semimajor axes also arises, leading to large-scale spreading of the planetesimal population throughout the inner regions of the protoplanetary disc, in apparent contradiction of constraints provided by the distribution of asteroids within the asteroid belt. In this paper, we examine the dynamics of planetesimals embedded in vertically stratified turbulent discs, with and without dead zones. Our main aims are to examine the turbulent excitation of the velocity dispersion, and the radial diffusion, of planetesimals in these discs. We employ three dimensional MHD simulations [...], along with an equilibrium chemistry model [...] We find that planetesimals in fully turbulent discs develop large random velocities that will lead to collisional destruction/erosion for bodies with sizes below 100 km, and undergo radial diffusion on a scale \sim 2.5 au over a 5 Myr disc life time. But planetesimals in a dead zone experience a much reduced excitation of their random velocities, and equilibrium velocity dispersions lie between the disruption thresholds for weak and strong aggregates for sizes R_p < 100 km. We also find that radial diffusion occurs over a much reduced length scale \sim 0.25 au over the disc life time, this being consistent with solar system constraints. We conclude that planetesimal growth via mutual collisions between smaller bodies cannot occur in a fully turbulent disc. By contrast, a dead zone may provide a safe haven in which km-sized planetesimals can avoid mutual destruction through collisions.Comment: 18 pages, 13 figures, 3 tables, MNRAS in press, minor corrections to match the published versio

Magnetic helicity fluxes in interface and flux transport dynamos

Dynamos in the Sun and other bodies tend to produce magnetic fields that possess magnetic helicity of opposite sign at large and small scales, respectively. The build-up of magnetic helicity at small scales provides an important saturation mechanism. In order to understand the nature of the solar dynamo we need to understand the details of the saturation mechanism in spherical geometry. In particular, we want to understand the effects of magnetic helicity fluxes from turbulence and meridional circulation. We consider a model with just radial shear confined to a thin layer (tachocline) at the bottom of the convection zone. The kinetic alpha owing to helical turbulence is assumed to be localized in a region above the convection zone. The dynamical quenching formalism is used to describe the build-up of mean magnetic helicity in the model, which results in a magnetic alpha effect that feeds back on the kinetic alpha effect. In some cases we compare with results obtained using a simple algebraic alpha quenching formula. In agreement with earlier findings, the magnetic alpha effect in the dynamical alpha quenching formalism has the opposite sign compared with the kinetic alpha effect and leads to a catastrophic decrease of the saturation field strength with increasing magnetic Reynolds numbers. However, at high latitudes this quenching effect can lead to secondary dynamo waves that propagate poleward due to the opposite sign of alpha. Magnetic helicity fluxes both from turbulent mixing and from meridional circulation alleviate catastrophic quenching.Comment: 9 pages, 14 figures, submitted to A &

On the dynamics of planetesimals embedded in turbulent protoplanetary discs

(abridged) Angular momentum transport and accretion in protoplanetary discs are generally believed to be driven by MHD turbulence via the magneto-rotational instability (MRI). The dynamics of solid bodies embedded in such discs (dust grains, boulders, planetesimals and planets) may be strongly affected by the turbulence, such that the formation pathways for planetary systems are determined in part by the strength and spatial distribution of the turbulent flow. We examine the dynamics of planetesimals, with radii between 1m \^a 10 km, embedded in turbulent protoplanetary discs, using three dimensional MHD simulations. The planetesimals experience gas drag and stochastic gravitational forces due to the turbulent disc. We use, and compare the results from, local shearing box simulations and global models in this study. The main aims of this work are to examine: the growth, and possible saturation, of the velocity dispersion of embedded planetesimals as a function of their size and disc parameters; the rate of radial migration and diffusion of planetesimals; the conditions under which the results from shearing box and global simulations agree. We find good agreement between local and global simulations when shearing boxes of dimension 4H x 16H x 2H are used (H being the local scale height). The magnitude of the density fluctuations obtained is sensitive to the box size, due to the excitation and propagation of spiral density waves. This affects the stochastic forcing experienced by planetesimals. [...] Our models show that fully developed MHD turbulence in protoplanetary discs would have a destructive effect on embedded planetesimals. Relatively low levels of turbulence are required for traditional models of planetesimal accretion to operate, this being consistent with the existence of a dead zone in protoplanetary discs.Comment: 23 pages, 28 figures, 3 tables, accepted for publication in MNRA