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

Mean-field and direct numerical simulations of magnetic flux concentrations from vertical field

Strongly stratified hydromagnetic turbulence has previously been found to produce magnetic flux concentrations if the domain is large enough compared with the size of turbulent eddies. Mean-field simulations (MFS) using parameterizations of the Reynolds and Maxwell stresses show a negative effective magnetic pressure instability and have been able to reproduce many aspects of direct numerical simulations (DNS) regarding the growth rate of this large-scale instability, shape of the resulting magnetic structures, and their height as a function of magnetic field strength. Unlike the case of an imposed horizontal field, for a vertical one, magnetic flux concentrations of equipartition strength with the turbulence can be reached. This results in magnetic spots that are reminiscent of sunspots. Here we want to find out under what conditions magnetic flux concentrations with vertical field occur and what their internal structure is. We use a combination of MFS, DNS, and implicit large-eddy simulations to characterize the resulting magnetic flux concentrations in forced isothermal turbulence with an imposed vertical magnetic field. We confirm earlier results that in the kinematic stage of the large-scale instability the horizontal wavelength of structures is about 10 times the density scale height. At later times, even larger structures are being produced in a fashion similar to inverse spectral transfer in helically driven turbulence. Using turbulence simulations, we find that magnetic flux concentrations occur for different values of the Mach number between 0.1 and 0.7. DNS and MFS show magnetic flux tubes with mean-field energies comparable to the turbulent kinetic energy. The resulting vertical magnetic flux tubes are being confined by downflows along the tubes and corresponding inflow from the sides, which keep the field concentrated.Comment: 16 pages, 22 figures, Astron. Astrophys., in pres

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 Hydromagnetic Simulations of Protoplanetary Disks with Stellar Irradiation and Simplified Thermochemistry

Outflows driven by large-scale magnetic fields likely play an important role in the evolution and dispersal of protoplanetary disks, and in setting the conditions for planet formation. We extend our 2-D axisymmetric non-ideal MHD model of these outflows by incorporating radiative transfer and simplified thermochemistry, with the twin aims of exploring how heating influences wind launching, and illustrating how such models can be tested through observations of diagnostic spectral lines. Our model disks launch magnetocentrifugal outflows primarily through magnetic tension forces, so the mass-loss rate increases only moderately when thermochemical effects are switched on. For typical field strengths, thermochemical and irradiation heating are more important than magnetic dissipation. We furthermore find that the entrained vertical magnetic flux diffuses out of the disk on secular timescales as a result of non-ideal MHD. Through post-processing line radiative transfer, we demonstrate that spectral line intensities and moment-1 maps of atomic oxygen, the HCN molecule, and other species show potentially observable differences between a model with a magnetically driven outflow and one with a weaker, photoevaporative outflow. In particular, the line shapes and velocity asymmetries in the moment-1 maps could enable the identification of outflows emanating from the disk surface.Comment: 35 pages, 20 figures, accepted for publication in Ap

Chandrasekhar-Kendall functions in astrophysical dynamos

Some of the contributions of Chandrasekhar to the field of magnetohydrodynamics are highlighted. Particular emphasis is placed on the Chandrasekhar-Kendall functions that allow a decomposition of a vector field into right- and left-handed contributions. Magnetic energy spectra of both contributions are shown for a new set of helically forced simulations at resolutions higher than what has been available so far. For a forcing function with positive helicity, these simulations show a forward cascade of the right-handed contributions to the magnetic field and nonlocal inverse transfer for the left-handed contributions. The speed of inverse transfer is shown to decrease with increasing value of the magnetic Reynolds number.Comment: 10 pages, 5 figures, proceedings of the Chandrasekhar Centenary Conference, to be published in PRAMANA - Journal of Physic

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

Low-Frequency Oscillations in Global Simulations of Black Hole Accretion

We have identified the presence of large-scale, low-frequency dynamo cycles in a long-duration, global, magnetohydrodynamic (MHD) simulation of black hole accretion. Such cycles had been seen previously in local shearing box simulations, but we discuss their evolution over 1,500 inner disk orbits of a global pi/4 disk wedge spanning two orders of magnitude in radius and seven scale heights in elevation above/below the disk midplane. The observed cycles manifest themselves as oscillations in azimuthal magnetic field occupying a region that extends into a low-density corona several scale heights above the disk. The cycle frequencies are ten to twenty times lower than the local orbital frequency, making them potentially interesting sources of low-frequency variability when scaled to real astrophysical systems. Furthermore, power spectra derived from the full time series reveal that the cycles manifest themselves at discrete, narrow-band frequencies that often share power across broad radial ranges. We explore possible connections between these simulated cycles and observed low-frequency quasi-periodic oscillations (LFQPOs) in galactic black hole binary systems, finding that dynamo cycles have the appropriate frequencies and are located in a spatial region associated with X-ray emission in real systems. Derived observational proxies, however, fail to feature peaks with RMS amplitudes comparable to LFQPO observations, suggesting that further theoretical work and more sophisticated simulations will be required to form a complete theory of dynamo-driven LFQPOs. Nonetheless, this work clearly illustrates that global MHD dynamos exhibit quasi-periodic behavior on timescales much longer than those derived from test particle considerations.Comment: Version accepted to The Astrophysical Journal, 8 pages, 7 figure

Simulations of galactic dynamos

We review our current understanding of galactic dynamo theory, paying particular attention to numerical simulations both of the mean-field equations and the original three-dimensional equations relevant to describing the magnetic field evolution for a turbulent flow. We emphasize the theoretical difficulties in explaining non-axisymmetric magnetic fields in galaxies and discuss the observational basis for such results in terms of rotation measure analysis. Next, we discuss nonlinear theory, the role of magnetic helicity conservation and magnetic helicity fluxes. This leads to the possibility that galactic magnetic fields may be bi-helical, with opposite signs of helicity and large and small length scales. We discuss their observational signatures and close by discussing the possibilities of explaining the origin of primordial magnetic fields.Comment: 28 pages, 15 figure, to appear in Lecture Notes in Physics "Magnetic fields in diffuse media", Eds. E. de Gouveia Dal Pino and A. Lazaria

Genetic load and transgenic mitigating genes in transgenic \u3ci\u3eBrassica rapa\u3c/i\u3e (field mustard) × \u3ci\u3eBrassica napus\u3c/i\u3e (oilseed rape) hybrid populations

Abstract Background One theoretical explanation for the relatively poor performance of Brassica rapa (weed) × Brassica napus (crop) transgenic hybrids suggests that hybridization imparts a negative genetic load. Consequently, in hybrids genetic load could overshadow any benefits of fitness enhancing transgenes and become the limiting factor in transgenic hybrid persistence. Two types of genetic load were analyzed in this study: random/linkage-derived genetic load, and directly incorporated genetic load using a transgenic mitigation (TM) strategy. In order to measure the effects of random genetic load, hybrid productivity (seed yield and biomass) was correlated with crop- and weed-specific AFLP genomic markers. This portion of the study was designed to answer whether or not weed × transgenic crop hybrids possessing more crop genes were less competitive than hybrids containing fewer crop genes. The effects of directly incorporated genetic load (TM) were analyzed through transgene persistence data. TM strategies are proposed to decrease transgene persistence if gene flow and subsequent transgene introgression to a wild host were to occur. Results In the absence of interspecific competition, transgenic weed × crop hybrids benefited from having more crop-specific alleles. There was a positive correlation between performance and number of B. napus crop-specific AFLP markers [seed yield vs. marker number (r = 0.54, P = 0.0003) and vegetative dry biomass vs. marker number (r = 0.44, P = 0.005)]. However under interspecific competition with wheat or more weed-like conditions (i.e. representing a situation where hybrid plants emerge as volunteer weeds in subsequent cropping systems), there was a positive correlation between the number of B. rapa weed-specific AFLP markers and seed yield (r = 0.70, P = 0.0001), although no such correlation was detected for vegetative biomass. When genetic load was directly incorporated into the hybrid genome, by inserting a fitness-mitigating dwarfing gene that that is beneficial for crops but deleterious for weeds (a transgene mitigation measure), there was a dramatic decrease in the number of transgenic hybrid progeny persisting in the population. Conclusion The effects of genetic load of crop and in some situations, weed alleles might be beneficial under certain environmental conditions. However, when genetic load was directly incorporated into transgenic events, e.g., using a TM construct, the number of transgenic hybrids and persistence in weedy genomic backgrounds was significantly decreased

Molecular Strategies for Gene Containment in Transgenic Crops

The potential of genetically modified (GM) crops to transfer foreign genes through pollen to related plant species has been cited as an environmental concern. Until more is known concerning the environmental impact of novel genes on indigenous crops and weeds, practical and regulatory considerations will likely require the adoption of gene-containment approaches for future generations of GM crops. Most molecular approaches with potential for controlling gene flow among crops and weeds have thus far focused on maternal inheritance, male sterility, and seed sterility. Several other containment strategies may also prove useful in restricting gene flow, including apomixis (vegetative propagation and asexual seed formation), cleistogamy (self-fertilization without opening of the flower), genome incompatibility, chemical induction/deletion of transgenes, fruit-specific excision of transgenes, and transgenic mitigation (transgenes that compromise fitness in the hybrid). As yet, however, no strategy has proved broadly applicable to all crop species, and a combination of approaches may prove most effective for engineering the next generation of GM crops