Particle module of Piernik MHD code

Piernik is a multi-fluid grid magnetohydrodynamic code based on the Relaxing Total Variation Diminishing conservative scheme. The original code has been extended by addition of the dust described within the particle approximation. The dust is now described as a system of interacting particles. The particles can interact with gas, which is described as a fluid. The comparison between the test problem results and the results coming from fluid simulations made with Piernik code shows the most important differences between fluid and particle approximations used to describe dynamical evolution of dust under astrophysical conditions

Bifurcation of planetary building blocks during Solar System formation

Geochemical and astronomical evidence demonstrate that planet formation occurred in two spatially and temporally separated reservoirs. The origin of this dichotomy is unknown. We use numerical models to investigate how the evolution of the solar protoplanetary disk influenced the timing of protoplanet formation and their internal evolution. Migration of the water snow line can generate two distinct bursts of planetesimal formation that sample different source regions. These reservoirs evolve in divergent geophysical modes and develop distinct volatile contents, consistent with constraints from accretion chronology, thermo-chemistry, and the mass divergence of inner and outer Solar System. Our simulations suggest that the compositional fractionation and isotopic dichotomy of the Solar System was initiated by the interplay between disk dynamics, heterogeneous accretion, and internal evolution of forming protoplanets.Comment: Published 21 January 2021; authors' version; 30 pages, 18 figures; summary available at http://bit.ly/BifurcationBlog (blog) and https://bit.ly/BifurcationVideo (video

Satellites Form Fast and Late: a Population Synthesis for the Galilean Moons

Stars and planetary system

2'-O-Methylation of the second transcribed nucleotide within the mRNA 5' cap impacts the protein production level in a cell-specific manner and contributes to RNA immune evasion

In mammals, m7G-adjacent nucleotides undergo extensive modifications. Ribose of the first or first and second transcribed nucleotides can be subjected to 2'-O-methylation to form cap1 or cap2, respectively. When the first transcribed nucleotide is 2'-O-methylated adenosine, it can be additionally modified to N6,2'-O-dimethyladenosine (m6Am). Recently, the crucial role of cap1 in distinguishing between 'self' and 'non-self' in mammalian cells during viral infection was revealed. Here, we attempted to understand the impact of cap methylations on RNA-related processes. Therefore, we synthesized tetranucleotide cap analogues and used them for RNA capping during in vitro transcription. Using this tool, we found that 2'-O-methylation of the second transcribed nucleotide within the mRNA 5' cap influences protein production levels in a cell-specific manner. This modification can strongly hamper protein biosynthesis or have no influence on protein production levels, depending on the cell line. Interestingly, 2'-O-methylation of the second transcribed nucleotide and the presence of m6Am as the first transcribed nucleotide serve as determinants that define transcripts as 'self' and contribute to transcript escape from the host innate immune response. Additionally, cap methylation status does not influence transcript affinity towards translation initiation factor eIF4E or in vitro susceptibility to decapping by DCP2; however, we observe the resistance of cap2-RNA to DXO (decapping exoribonuclease)-mediated decapping and degradation.publishe

Purification of eukaryotic exoribonucleases following heterologous expression in bacteria and analysis of their biochemical properties by in vitro enzymatic assays

Exoribonucleases-among the other RNases-play a crucial role in the regulation of different aspects of RNA metabolism in the eukaryotic cell. To fully understand the exact mechanism of activity exhibited by such enzymes, it is crucial to determine their detailed biochemical properties, notably their substrate specificity and optimal conditions for enzymatic action. One of the most significant features of exoribonucleases is the direction of degradation of RNA substrates, which can proceed either from 5'-end to 3'-end or in the opposite way. Here, we present methods allowing the efficient production and purification of eukaryotic exoribonucleases, the preparation and labeling of various RNA substrates, and the biochemical characterization of exonucleolytic activity. We also explain how the exonucleolytic activity may be distinguished from that of endonucleases

The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L

The eukaryotic RNA exosome is a ribonucleolytic complex involved in RNA processing and turnover. It consists of a nine-subunit catalytically inert core that serves a structural function and participates in substrate recognition. Best defined in Saccharomyces cerevisiae, enzymatic activity comes from the associated subunits Dis3p (Rrp44p) and Rrp6p. The former is a nuclear and cytoplasmic RNase II/R-like enzyme, which possesses both processive exo- and endonuclease activities, whereas the latter is a distributive RNase D-like nuclear exonuclease. Although the exosome core is highly conserved, identity and arrangements of its catalytic subunits in different vertebrates remain elusive. Here, we demonstrate the association of two different Dis3p homologs—hDIS3 and hDIS3L—with the human exosome core. Interestingly, these factors display markedly different intracellular localizations: hDIS3 is mainly nuclear, whereas hDIS3L is strictly cytoplasmic. This compartmental distribution reflects the substrate preferences of the complex in vivo. Both hDIS3 and hDIS3L are active exonucleases; however, only hDIS3 has retained endonucleolytic activity. Our data suggest that three different ribonucleases can serve as catalytic subunits for the exosome in human cells