Gutenberg-Richter’s law in sliding friction of gels

We report on experimental studies of spatio-temporally heterogeneous stick-slip motions in the sliding friction between a hard polymethyl methacrylate (PMMA, plexiglass) block and a soft poly-dimethyl siloxane (PDMS, silicone) gel plate. We perform experiments on two PDMS gels with different viscoelastic properties. For the less viscous gel, large and rapid events are preceded by an alternation of active and less active periods. For the more viscous gel, successive slow slip events take place continuously. The probability distributions of the force drop, a quantity analogous to seismic moment, obey a power law similar to Gutenberg-Richter's empirical law for the frequency-size statistics of earthquakes, and the exponents of the power law vary with the plate velocity and the viscosity of the gel. We propose a simple model to explain the dependence of the power law exponent on the plate velocity, which agrees with experimental results

Experiments on the Entrainment of Sediment by Turbidity Currents with the Use of Submarine Sediment

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchiv

Spatial and temporal turbidity currents sediment deposition assessment

Flume experiments are conducted to model sediment-laden density currents with continuous suspension supply. The initial density covers 1008, 1016, and 1032 kg/m3 and the bottom slope at 5.0 %. Sediment deposition profiles along the experimental flume are measured using an electrical resistance-based depositometer (ERBD). The measurement technique is described, its calibration procedure is presented and results shown. The discussion highlights the influence of the initial turbidity currents density respectively suspension concentration as well as the flow dynamics of the currents. After head passage, the main deposition takes place in the body and linear deposition pattern along the flume axis is observed

Sediment mass movement of a particle-laden turbidity current based on ultrasound velocity profiling and the distribution of sediment concentration

Particle-laden flows or turbidity currents along the seafloor are important to the formation and erosion of submarine topography. To understand the mass-transport process, flume tests were carried out with a continuous supply of quartz-laden suspension. The vertical and horizontal velocities were extracted by two pairs of ultrasound Doppler velocity profilers installed at different angles with respect to the bed-normal direction. Due to the head intrusion into the ambient water, the sediment in the suspension was continuously lifted up and mixed, leaving lobes and clefts. The velocity-maximum layer acted as the main sediment conveyor and divided the body into wall and jet regions. The concentration distribution was also quantified based on the Relationship between the fluid density and the intensity of light attenuation obtained using a video recording. An area of high sediment concentration was observed just behind the head frontal area. Analysis of the velocity and concentration distribution demonstrated that sediment in the turbidity current was transported mainly by head movement and that continuous sedimentation took place in the wall region. The results indicate that a turbidity current proceeds while maintaining an ordered inner dynamic structure

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

Naturally occurring regulatory T (Treg) cells, which specifically express the transcription factor forkhead box P3 (Foxp3), are engaged in the maintenance of immunological self-tolerance and homeostasis. By transcriptional start site cluster analysis, we assessed here how genome-wide patterns of DNA methylation or Foxp3 binding sites were associated with Treg-specific gene expression. We found that Treg-specific DNA hypomethylated regions were closely associated with Treg up-regulated transcriptional start site clusters, whereas Foxp3 binding regions had no significant correlation with either up- or down-regulated clusters in nonactivated Treg cells. However, in activated Treg cells, Foxp3 binding regions showed a strong correlation with down-regulated clusters. In accordance with these findings, the above two features of activation-dependent gene regulation in Treg cells tend to occur at different locations in the genome. The results collectively indicate that Treg-specific DNA hypomethylation is instrumental in gene up-regulation in steady state Treg cells, whereas Foxp3 down-regulates the expression of its target genes in activated Treg cells. Thus, the two events seem to play distinct but complementary roles in Treg-specific gene expression

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism