Nucleus-cytoskeleton communication impacts on OCT4-chromatin interactions in embryonic stem cells

Background The cytoskeleton is a key component of the system responsible for transmitting mechanical cues from the cellular environment to the nucleus, where they trigger downstream responses. This communication is particularly relevant in embryonic stem (ES) cells since forces can regulate cell fate and guide developmental processes. However, little is known regarding cytoskeleton organization in ES cells, and thus, relevant aspects of nuclear-cytoskeletal interactions remain elusive. Results We explored the three-dimensional distribution of the cytoskeleton in live ES cells and show that these filaments affect the shape of the nucleus. Next, we evaluated if cytoskeletal components indirectly modulate the binding of the pluripotency transcription factor OCT4 to chromatin targets. We show that actin depolymerization triggers OCT4 binding to chromatin sites whereas vimentin disruption produces the opposite effect. In contrast to actin, vimentin contributes to the preservation of OCT4-chromatin interactions and, consequently, may have a pro-stemness role. Conclusions Our results suggest roles of components of the cytoskeleton in shaping the nucleus of ES cells, influencing the interactions of the transcription factor OCT4 with the chromatin and potentially affecting pluripotency and cell fate.

Measurement report: Vehicle-based multi-lidar observational study of the effect of meteorological elements on the three-dimensional distribution of particles in the western Guangdong–Hong Kong–Macao Greater Bay Area

The distribution of meteorological elements has always been an important factor in determining the horizontal and vertical distribution of particles in the atmosphere. To study the effect of meteorological elements on the three-dimensional distribution structure of particles, mobile vehicle lidar and fixed-location observations were collected in the western Guangdong–Hong Kong–Macao Greater Bay Area of China during September and October in 2019 and 2020. Vertical aerosol extinction coefficient, depolarization ratio, and wind and temperature profiles were measured using a micro pulse lidar, a Raman scattering lidar, and a Doppler wind profile lidar installed on a mobile monitoring vehicle. The mechanism of how wind and temperature in the boundary layer affects the horizontal and vertical distribution of particles was analysed. The results show that particles were mostly distributed in downstream areas on days with moderate wind speed in the boundary layer, whereas they were distributed homogeneously on days with weaker wind. There are three typical types of vertical distribution of particles in the western Guangdong–Hong Kong–Macao Greater Bay Area (GBA): surface single layer, elevated single layer, and double layer. Analysis of wind profiles and Hybrid Single-Particle Lagrangian Integrated Trajectory Model (HYSPLIT) backward trajectory reveals different sources of particles for the three types. Particles concentrating near the temperature inversion and multiple inversions could cause more than one peak in the extinction coefficient profile. There were two mechanisms affecting the distribution of particulate matter in the upper and lower boundary layers. Based on this observational study, a general model of meteorological elements affecting the vertical distribution of urban particulate matter is proposed.

Measuring the Similarity of Metro Stations Based on the Passenger Visit Distribution

The distribution of passengers reflects the characteristics of urban rail stations. The automatic fare collection system of rail transit collects a large amount of passenger trajectory data tracking the entry and exit continuously, which provides a basis for detailed passenger distributions. We first exploit the Automatic Fare Collection (AFC) data to construct the passenger visit pattern distribution for stations. Then we measure the similarity of all stations using Wasserstein distance. Different from other similarity metrics, Wasserstein distance takes the similarity between values of quantitative variables in the one-dimensional distribution into consideration and can reflect the correlation between different dimensions of high-dimensional data. Even though the computational complexity grows, it is applicable in the metro stations since the scale of urban rail transit stations is limited to tens to hundreds and detailed modeling of the stations can be performed offline. Therefore, this paper proposes an integrated method that can cluster multi-dimensional joint distribution considering similarity and correlation. Then this method is applied to cluster the rail transit stations by the passenger visit distribution, which provides some valuable insight into the flow management and the station replanning of urban rail transit in the future.

An experiment design for schools to demonstrate the Maxwell distribution

The article describes a new version of a demonstration experiment for the Maxwell distribution. In the first part students analyse the applicability of the Gaussian distribution to the projection of the particle velocities in the suggested experiment. Further, students observe two-dimensional distribution of particles by the modulus of velocity in a mechanical demonstration model and compare the results with theoretical provisions. Demonstration of the two-dimensional version of the Maxwell distribution for particle interaction allows students to independently derive formulas for the three-dimensional Maxwell distribution for particles in an ideal gas. The use of the suggested demonstration ensures active engagement in fundamentally important physical content.

Parameterized orographic gravity wave drag in CMIP6 models, distribution, variability, trends and intermodel spread

<p>Internal gravity waves (GWs) are a naturally occurring and intermittent phenomenon in the atmosphere. GWs can propagate horizontally and vertically and are important for atmospheric dynamics, influencing the atmospheric thermal and dynamical structure. Research on GWs is connected with some of the most challenging issues of Earth climate and atmospheric science. Consideration of GW-related processes is necessary for a proper description and modelling of the middle and upper atmosphere. However, as GWs exist on scales from a few to thousands of kilometers, they cannot be fully resolved by general circulation models (GCMs) and hence have to be parameterized. Although recently satellite and reanalysis datasets with improved resolution and novel analysis methods together with high-resolution atmospheric models have been tightening the constraints for GW parameterizations in GCMs, the parameterized GW effects still bear a significant margin of uncertainty.</p> <p>To quantify this uncertainty, we analyze the three-dimensional distribution and interannual variability of orographic gravity wave drag (OGWD) in chemistry-climate model simulations. For this, we use a set of AMIP simulations produced within the CMIP6 activity. In particular, we focus on the intermodel spread in the vertical and horizontal OGWD distribution. The different models generaly agree on the areas of the OGWD hotspots. However, in all these regions we find considerable intermodel differences in OGWD magnitude as well as in the altitude of the strongest GW dissipation. In this presentation, we show our findings and discuss possible explanations for the intermodel differences, like different parametrization schemes and choices of tunable parameters.</p>

MagIC v5.10: a two-dimensional message-passing interface (MPI) distribution for pseudo-spectral magnetohydrodynamics simulations in spherical geometry

We discuss two parallelization schemes for MagIC, an open-source, high-performance, pseudo-spectral code for the numerical solution of the magnetohydrodynamics equations in a rotating spherical shell. MagIC calculates the non-linear terms on a numerical grid in spherical coordinates, while the time step updates are performed on radial grid points with a spherical harmonic representation of the lateral directions. Several transforms are required to switch between the different representations. The established hybrid parallelization of MagIC uses message-passing interface (MPI) distribution in radius and relies on existing fast spherical transforms using OpenMP. Our new two-dimensional MPI decomposition implementation also distributes the latitudes or the azimuthal wavenumbers across the available MPI tasks and compute cores. We discuss several non-trivial algorithmic optimizations and the different data distribution layouts employed by our scheme. In particular, the two-dimensional distribution data layout yields a code that strongly scales well beyond the limit of the current one-dimensional distribution. We also show that the two-dimensional distribution implementation, although not yet fully optimized, can already be faster than the existing finely optimized hybrid parallelization when using many thousands of CPU cores. Our analysis indicates that the two-dimensional distribution variant can be further optimized to also surpass the performance of the one-dimensional distribution for a few thousand cores.

Distribution of Biominerals and Mineral-Organic Composites in Plant Trichomes

Biomineralization is a common phenomenon in plants and has been shown to be chemically, functionally and topologically diverse. Silica and calcium carbonate have long been known as structural plant biominerals and calcium phosphate (apatite)–long known from animals–has recently been reported. Strikingly, up to three different biominerals may occur in a single trichome in, e.g., Urticaceae and Loasaceae, and in combination with organic compounds, can form organic/inorganic composite materials. This article presents an extension of previous studies on the distribution of these biominerals in Loasaceae trichomes with a focus on their spatial (three-dimensional) distribution and co-localization with organic substances. Light microscopy and scanning electron microscopy with high-resolution EDX element analyses of sample surfaces and sections illustrate the differential distribution and composition of the different biomineral phases across cell surfaces and cell walls. Raman spectroscopy additionally permits the identification of organic and inorganic compounds side by side. All three biominerals may be found in a nearly pure inorganic phase, e.g., on the plant surfaces and in the barbs of the glochidiate trichomes, or in combination with a larger proportion of organic compounds (cellulose, pectin). The cell lumen may be additionally filled with amorphous mineral deposits. Water-solubility of the mineral fractions differs considerably. Plant trichomes provide an exciting model system for biomineralization and enable the in-vivo study of the formation of complex composite materials with different biomineral and organic compounds involved.

Double-layered two-directional somatopleural cell migration during chicken body wall development revealed with local fluorescent tissue labeling

The ventral body wall is derived from the somatic layer of the lateral plate mesoderm, somatopleure, and somite. The primary ventral body wall is formed as a result of the lateral growth of the somatopleure. The secondary body wall is generated through the migration of somitic cells into the somatopleure. While it is reported that the cervical somatopleural cells migrate caudally to the thoracic region during body wall development, the migration of the thoracic somatopleural cells has not been elucidated. To investigate the migration behavior of the somatopleural cells in the thorax during chicken ventral body wall development, we labeled the thoracic somatopleural cells of one somite wide by DiI labeling or gene transfection of enhanced green fluorescent protein and observed the three-dimensional distribution of the labeled cells with the tissue-clearing technique FRUIT. Our labeling experiments revealed the rostral migration of the somatopleural cells into a deep part of the thoracic body wall in embryonic day 6.5 chickens. For embryonic day 8.5 chickens, these deep migrating somatopleural cells were found around the sternal ribs. Thus, we identified the double-layered two-directional migrating pathways of the somatopleural cells: the rostral migration of the deep somatopleural cells and the lateral migration of the superficial somatopleural cells. Our findings imply that the rostral migration of deep somatopleural cells and the lateral migration of superficial ones might be associated with the developing sternal ribs and the innervation of the thoracic cutaneous nerves, respectively.