Transcriptional burst kinetics are linked to short term transcriptional memory

Transcriptional bursting is thought to be a stochastic process that allows the dynamic regulation of most genes. The random telegraph model assumes the existence of two states, ON and OFF. However recent studies indicate the presence of additional ON states, suggesting that bursting kinetics and their regulation can be quite complex. We have developed a system to study transcriptional bursting in the context of p53 biology using the endogenous p21 gene tagged with MS2 in human cells. Remarkably, we find that transcriptional bursts from the p21 gene contain multiple ON and OFF states that can be regulated by elevation of p53 levels. Distinct ON states are characterized by differences in burst duration, classified as Short and Long, with long bursts associated with higher Pol II initiation rates. Importantly, the different ON states display memory effects that allow us to predict the likelihood of properties of future bursting events. Long bursting events result in faster re-activation, longer subsequent bursts and higher transcriptional output in the future compared to short bursts. Bursting memory persists up to 2 hours suggesting a stable inheritable promoter architecture. Bursting memory at the p21 gene is the strongest under basal conditions and is suppressed by UV and inhibition of H3K9me1/2, which also increase transcriptional noise. Stabilization of p53 by Nutlin-3a partially reverses suppression of bursting memory suggesting that higher p53 levels may be a key in enforcing memory under conditions of cellular stress. Overall our data uncover a new found bursting property termed Short-Term Transcriptional Memory (STTM) that has the potential to fine-tune transcriptional output at the p21 gene.

Understanding the Role of Sensorimotor Beta Oscillations

Beta oscillations have been predominantly observed in sensorimotor cortices and basal ganglia structures and they are thought to be involved in somatosensory processing and motor control. Although beta activity is a distinct feature of healthy and pathological sensorimotor processing, the role of this rhythm is still under debate. Here we review recent findings about the role of beta oscillations during experimental manipulations (i.e., drugs and brain stimulation) and their alteration in aging and pathology. We show how beta changes when learning new motor skills and its potential to integrate sensory input with prior contextual knowledge. We conclude by discussing a novel methodological approach analyzing beta oscillations as a series of transient bursting events.

Dynamics of vesicle reshaping and scission under osmotic shocks

We study the effects of osmotic shocks on lipid vesicles via coarse-grained molecular dynamics simulations by explicitly considering the solute in the system. We find that depending on their nature (hypo- or hypertonic) such shocks can lead to bursting events or engulfing of external material into inner compartments, among other morphology transformations. We characterize the dynamics of these processes and observe a separation of time scales between the osmotic shock absorption and the shape relaxation. Our work consequently provides an insight into the dynamics of compartmentalization in vesicular systems as a result of osmotic shocks, which can be of interest in the context of early proto-cell development and proto-cell compartmentalisation.

Study of bursting events and effect of hole-size on turbulent bursts triggered by the fluid and mid-channel bar interaction

Turbulent structures of flow around the mid-channel braid bar have not been adequately investigated so far. Of late, the intrinsic fluvial hydraulics associated with the formation of braided rivers interspersed with sand bars have been vital topics of research. In this paper, the findings yielded from a research foray on the aforementioned underlying processes are presented. For obtaining the requisite experimental data, the three-dimensional flow velocity components are measured with the help of acoustic Doppler velocimetry (ADV) and these velocity data are analyzed using quadrant bursting techniques. The flow characteristics are greatly affected by the presence of a mid-channel bar. The depth-averaged contours of turbulent parameters are analyzed in the present study. Herein, the hole size concept is adopted for separating the bursting events. The effect of hole size on the quadrant events is also studied. The experiments are performed for different submergence ratios. A new parameter, Bursting Index (BI), is proposed in this research to reflect a quantitative measure of the turbulent bursting effect on streambed elevation changes. The parameter BI is the ratio of the odd event occurrence probability to the even event occurrence probability. The high values of correlation coefficients signify that the BI is profoundly influenced by streambed elevation changes, which makes it an ideal parameter for analyzing scour and deposition phenomena in real-life water management projects. The prime focus on performing the experiments has been to analyze the impact of bar height on flow structure in the vicinity of the mid-channel bar.

Shoaling Waves Interacting with an Orthogonal Current

In the present work, an experimental investigation on the hydrodynamics of shoaling waves superposed on a steady orthogonal current is carried out. An experimental campaign in a wave tank has been performed, with waves and current interacting at a right angle over a sloping planar beach. Velocity data have been gathered during the experiments in order to investigate mean, phase and turbulent flow. A detailed preliminary analysis of the time- and space-variability of the experiments is presented. Results show that a complex interaction between waves and current occurs as the wave shoals, in terms of sheer production, momentum transfer and turbulent mixing. Superposition of waves determines a shear increase at the bottom due to an enhanced turbulence mixing, nonetheless as depth decreases and the current velocity consequently increases, shoaling waves may be less efficient in enhancing shear at the bottom. Moreover, the superposition of waves determines the current to oscillate around its mean velocity value. Nevertheless, as wave shoals and simultaneously current velocity increases with decreasing depth, waves and current oscillatory motion experience a phase lag, as a response of the larger momentum of the current to the changing of the shoaling waves acceleration distribution along the wave phase. Moreover, the turbulent bursting events of the combined flow in proximity of the bed have been investigated by means of quadrant analysis, showing an increase of the turbulent ejections and sweeps due to the superposition of the shoaling waves.

The characteristics and mechanism of microbubble drag reduction on the axisymmetric body

To investigate the characteristics and mechanism of microbubble drag reduction on the axisymmetric body, both experiments and the numerical simulation of microbubble drag reduction have been conducted in this paper. Based on the experiments, the morphology of microbubble flow and the characteristics of microbubble drag reduction were analyzed. The size distribution of microbubbles and the influence of microbubble size on the drag reduction efficiency were quantitatively investigated. Based on the numerical simulation, the influences of microbubbles on the turbulence intensity and vorticity were analyzed to investigate the mechanism of microbubble drag reduction. The results indicate that the diameters of microbubbles basically obey the normal distribution at various conditions, and the microbubble flow presents the uniform microbubble, roll-up and cavity. As the air injection rate increases, the drag reduction respectively shows microbubble drag reduction, mixture drag reduction and air-layer drag reduction. Besides, the drag reduction ratio correspondingly presents the increasing stage, rapidly increasing stage and stable stage. At the same void ratio, the smaller microbubbles show the higher efficiency in drag reduction. The microbubbles injected into the boundary layer can reduce the turbulence intensity and the frequency of the bursting events in the flow field, which results in the drag reduction.