Kyle Gustafson

Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells

Circadian cycles and cell cycles are two fundamental periodic processes with a period in the range of 1 day. Consequently, coupling between such cycles can lead to synchronization. Here, we estimated the mutual interactions between the two oscillators by time‐lapse imaging of single mammalian NIH3T3 fibroblasts during several days. The analysis of thousands of circadian cycles in dividing cells clearly indicated that both oscillators tick in a 1:1 mode‐locked state, with cell divisions occurring tightly 5 h before the peak in circadian Rev‐Erbα‐YFP reporter expression. In principle, such synchrony may be caused by either unidirectional or bidirectional coupling. While gating of cell division by the circadian cycle has been most studied, our data combined with stochastic modeling unambiguously show that the reverse coupling is predominant in NIH3T3 cells. Moreover, temperature, genetic, and pharmacological perturbations showed that the two interacting cellular oscillators adopt a synchronized state that is highly robust over a wide range of parameters. These findings have implications for circadian function in proliferative tissues, including epidermis, immune cells, and cancer.

Electrostatic instabilities, turbulence and fast ion interactions in the TORPEX device

Electrostatic turbulence, related structures and their effect on particle, heat and toroidal momentum transport are investigated in TORPEX simple magnetized plasmas using high-resolution diagnostics, control parameters, linear fluid models and nonlinear numerical simulations. The nature of the dominant instabilities is controlled by the value of the vertical magnetic field, Bv, relative to that of the toroidal field, BT. For Bv/BT > 3%, only ideal interchange instabilities are observed. A critical pressure gradient to drive the interchange instability is experimentally identified. Interchange modes give rise to blobs, radially propagating filaments of enhanced plasma pressure. Blob velocities and sizes are obtained from electrostatic probe measurements using pattern recognition methods. The observed values span a wide range and are described by a single analytical expression, from the small blob size regime in which the blob velocity is limited by cross-field ion polarization currents, to the large blob size regime in which the limitation to the blob velocity comes from parallel currents to the sheath. As a first attempt at controlling the blob dynamical properties, limiter configurations with varying angles between field lines and the conducting surface of the limiter are explored. Mach probe measurements clearly demonstrate a link between toroidal flows and blobs. To complement probe data, a fast framing camera and a movable gas puffing system are installed. Density and light fluctuations show similar signatures of interchange activity. Further developments of optical diagnostics, including an image intensifier and laser-induced fluorescence, are under way. The effect of interchange turbulence on fast ion phase space dynamics is studied using movable fast ion source and detector in scenarios for which the development from linear waves into blobs is fully characterized. A theory validation project is conducted in parallel with TORPEX experiments, based on quantitative comparisons of observables that are defined in the same way in the data and in the output of numerical codes, including 2D and 3D local and global simulations.

Nondiffusive Suprathermal Ion Transport in Simple Magnetized Toroidal Plasmas

We investigate suprathermal ion dynamics in simple magnetized toroidal plasmas in the presence of electrostatic turbulence driven by the ideal interchange instability. Turbulent fields from fluid simulations are used in the nonrelativistic equation of ion motion to compute suprathermal tracer ion trajectories. Suprathermal ion dispersion starts with a brief ballistic phase, during which particles do not interact with the plasma, followed by a turbulence interaction phase. In this one simple system, we observe the entire spectrum of suprathermal ion dynamics, from subdiffusion to superdiffusion, depending on beam energy and turbulence amplitude. We estimate the duration of the ballistic phase and identify basic mechanisms during the interaction phase that determine the dependencies of the character of suprathermal ion dispersion upon the beam energy and turbulence fluctuation amplitude.

Transport equation describing fractional Lévy motion of suprathermal ions in TORPEX

Suprathermal ions, created by fusion reactions or by additional heating, will play an important role in burning plasmas such as the ones in ITER or DEMO. Basic plasma experiments, with easy access for diagnostics and well-controlled plasma scenarios, are particularly suitable to investigate the transport of suprathermal ions in plasma waves and turbulence. Experimental measurements and numerical simulations have revealed that the transport of fast ions in the presence of electrostatic turbulence in the basic plasma toroidal experiment TORPEX is generally non-classical. Namely, the mean-squared radial displacement of the ions does not scale linearly with time, but 〈r2(t)〉 tγ, with γ ≠ 1 generally, γ > 1 corresponding to superdiffusion and γ < 1 to subdiffusion. A generalization of the classical model of diffusion, the so-called fractional Levy motion, which encompasses power-law (Levy) statistics for the displacements and correlated temporal increments, leads to non-classical dynamics such as that observed in the experiments. On a macroscopic scale, this results in fractional differential operators, which are used to model non-Gaussian, non-local anomalous transport in a growing number of applied fields, including plasma physics. In this paper, we show that asymmetric fractional Levy motion can be described by a diffusion equation using space-fractional differential operator with skewness. Numerical simulations of tracers in TORPEX turbulence are performed. The time evolution of the radial particle position distribution is shown to be described by solutions of the fractional diffusion equation corresponding to asymmetric fractional Levy motion in sub- and superdiffusive cases.

Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

BackgroundIn mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles that can portray the progression of PolII through sequential promoter states.ResultsHere, we analyze PolII binding profiles from high-coverage ChIP-seq on promoters of actively transcribed genes in mouse and humans. We show that the enrichment of PolII near transcription start sites exhibits a stereotypical bimodal structure, with one peak near active transcription start sites and a second peak 110 base pairs downstream from the first. Using an empirical model that reliably quantifies the spatial PolII signal, gene by gene, we show that the first PolII peak allows for refined positioning of transcription start sites, which is corroborated by mRNA sequencing. This bimodal signature is found both in mouse and humans. Analysis of the pausing-related factors NELF and DSIF suggests that the downstream peak reflects widespread pausing at the +1 nucleosome barrier. Several features of the bimodal pattern are correlated with sequence features such as CpG content and TATA boxes, as well as the histone mark H3K4me3.ConclusionsWe thus show how high coverage DNA sequencing experiments can reveal as-yet unnoticed bimodal spatial features of PolII accumulation that are frequent at individual mammalian genes and reminiscent of transcription initiation and pausing. The initiation-pausing hypothesis is corroborated by evidence from run-on sequencing and immunoprecipitation in other cell types and species.

Lévy walk description of suprathermal ion transport

Transport of suprathermal ions is examined from the Levy walk perspective in a simple magnetized toroidal plasma. Depending on their energy, these suprathermal ions exhibit superdiffusive, diffusive, or subdiffusive dispersion as a result of the complex interplay between ion drifts related to the magnetic field configuration and interaction of the ions with the plasma turbulence. By implementing a diagnostic that translates the ion trajectories into sequences of steps, we successfully describe their microscale dynamics as a Levy walk process. Previous analytical predictions that link the microscale Levy walk parameters to the macroscale suprathermal ion transport are confirmed for all observed regimes of ion dispersion. Additionally, we employ a statistical Levy walk generator for a direct comparison between transport of Levy walkers and of suprathermal ions, further validating the Levy walk description.

Investigation of fast ion transport in TORPEX

Basic aspects of fast ion transport in ideal interchange-mode unstable plasmas are investigated in the simple toroidal plasma device TORPEX. Fast ions are generated by a miniaturized lithium 6+ ion source with energies up to 1 keV, and are detected using a double-gridded energy analyser mounted on a two-dimensional movable system in the poloidal cross-section. The signal-to-noise ratio is enhanced by applying a modulated biasing voltage to the fast ion source and using a synchronous detection scheme. An analogue lock-in amplifier has been developed, which allows removing the capacitive noise associated with the voltage modulation. We characterize vertical and radial transport of the fast ions, which is associated with the plasma turbulence. Initial experimental results show good agreement with numerical simulations of the fast ion transport in a global fluid simulation of the TORPEX plasma.

Basic investigations of electrostatic turbulence and its interaction with plasma and suprathermal ions in a simple magnetized toroidal plasma

Progress in basic understanding of turbulence and its influence on the transport both of the plasma bulk and of suprathermal components is achieved in the TORPEX simple magnetized torus. This configuration combines a microwave plasma production scheme with a quasi-equilibrium generated by a toroidal magnetic field, onto which a small vertical component is superimposed, simulating a simplified form of tokamak scrape-off layers. After having clarified the formation of blobs in ideal interchange turbulence, TORPEX experiments elucidated the mechanisms behind the blob motion, with a general scaling law relating their size and speed. The parallel currents associated with the blobs, responsible for the damping of the charge separation that develops inside them, hence determining their cross-field velocity, have been measured. The blob dynamics is influenced by creating convective cells with biased electrodes, arranged in an array on a metal limiter. Depending on the biasing scheme, radial and vertical blob velocities can be varied. Suprathermal ion transport in small-scale turbulence is also investigated on TORPEX. Suprathermal ions are generated by a miniaturized lithium source, and are detected using a movable double-gridded energy analyser. We characterize vertical and radial spreading of the ion beam, associated with the ideal interchange-dominated plasma turbulence, as a function of the suprathermal ion energy and the plasma temperature. Experimental results are in good agreement with global fluid simulations, including in cases of non-diffusive behaviour. To investigate the interaction of plasma and suprathermal particles with instabilities and turbulence in magnetic configurations of increasing complexity, a closed field line configuration has recently been implemented on TORPEX, based on a current-carrying wire suspended in the vacuum chamber. First measurements indicate the creation of circular symmetric profiles centred on the magnetic axis, and instabilities driven in the region of strong gradients, with a strong ballooning character.

Plasma turbulence, suprathermal ion dynamics and code validation on the basic plasma physics device TORPEX

The TORPEX basic plasma physics device at the Center for Plasma Physics Research (CRPP) in Lausanne, Switzerland is described. In TORPEX, simple magnetized toroidal configurations, a paradigm for the tokamak scrape-off layer (SOL), as well as more complex magnetic geometries of direct relevance for fusion are produced. Plasmas of different gases are created and sustained by microwaves in the electron-cyclotron (EC) frequency range. Full diagnostic access allows for a complete characterization of plasma fluctuations and wave fields throughout the entire plasma volume, opening new avenues to validate numerical codes. We detail recent advances in the understanding of basic aspects of plasma turbulence, including its development from linearly unstable electrostatic modes, the formation of filamentary structures, or blobs, and its influence on the transport of energy, plasma bulk and suprathermal ions. We present a methodology for the validation of plasma turbulence codes, which focuses on quantitative assessment of the agreement between numerical simulations and TORPEX experimental data.

Three-dimensional measurements of non-diffusive fast ion transport in TORPEX

In the basic plasma physics device TORPEX, progress in the fundamental understanding of supra-thermal ion transport is achieved by extensive sets of three-dimensional (3D) data, together with numerical simulations of supra-thermal ion tracers in fluid turbulent fields. A miniaturized lithium 6+ ion source injects fast ions with energies up to 1 KeV and a double-gridded energy analyzer is used as a detector. The source is mounted on a toroidally movable system and the detector can be moved in the poloidal cross-section, allowing one to reconstruct 3D fast ion current profiles. Synchronous detection is used to enhance the signal-to-noise ratio. A modulated biasing voltage is applied to the fast ion source and an analog lock-in amplifier is used to demodulate the detector signal. The analog lock-in amplifier is specially designed to remove the capacitive noise associated with the voltage modulation. Radial transport of the fast ions, associated with plasma turbulence, is characterized. A synthetic diagnostic allows comparing the experimental results with numerical simulations of the fast ion transport in a global fluid simulation of the TORPEX plasma. A good agreement is shown.