Herwig++ 2.0 Release Note

A new release of the Monte Carlo program Herwig++ (version 2.0) is now available. This is the first version of the program which can be used for hadron-hadron physics and includes the full simulation of both initial- and final-state QCD radiation.Comment: Source code and additional information available at http://hepforge.cedar.ac.uk/herwig

The splicing landscape is globally reprogrammed during male meiosis

Meiosis requires conserved transcriptional changes, but it is not known whether there is a corresponding set of RNA splicing switches. Here, we used RNAseq of mouse testis to identify changes associated with the progression from mitotic spermatogonia to meiotic spermatocytes. We identified ∼150 splicing switches, most of which affect conserved protein-coding exons. The expression of many key splicing regulators changed in the course of meiosis, including downregulation of polypyrimidine tract binding protein (PTBP1) and heterogeneous nuclear RNP A1, and upregulation of nPTB, Tra2β, muscleblind, CELF proteins, Sam68 and T-STAR. The sequences near the regulated exons were significantly enriched in target sites for PTB, Tra2β and STAR proteins. Reporter minigene experiments investigating representative exons in transfected cells showed that PTB binding sites were critical for splicing of a cassette exon in the Ralgps2 mRNA and a shift in alternative 5′ splice site usage in the Bptf mRNA. We speculate that nPTB might functionally replace PTBP1 during meiosis for some target exons, with changes in the expression of other splicing factors helping to establish meiotic splicing patterns. Our data suggest that there are substantial changes in the determinants and patterns of alternative splicing in the mitotic-to-meiotic transition of the germ cell cycle

Initial (March 2023) uses and perceptions of ChatGPT in a sample of students and instructors at the University of Bergen (UiB), Norway

The spring semester of 2023 in higher education was impacted by the release of Large Language Models (LLMs) to the general public. OpenAI’s ChatGPT was at the forefront, with Google's Bard, Microsoft’s Bing, and others following suit. In response to the ongoing discussions in higher education, we conducted a survey to examine the use and understanding of LLMs among students and instructors at the Faculty of Mathematics and Natural Sciences at the University of Bergen, Norway. Given that the survey was distributed in February and March 2023 - shortly after ChatGPT was launched and before similar tools from other providers were in wide use - we focused primarily on ChatGPT. Our aim was to gain a deeper understanding of existing perceptions and misconceptions about ChatGPT, enabling us to design more informed implementation strategies for its integration into our courses. Further, by considering usage patterns and perceptions shortly after the launch of ChatGPT, we established a baseline for later comparisons as these tools become increasingly embedded in our routines.bioCEED, SLATEpublishedVersio

Deep conservation of ribosome stall sites across RNA processing genes

The rate of translation can vary depending on the mRNA template. During the elongation phase the ribosome can transiently pause or permanently stall. A pause can provide the nascent protein with the time to fold or be transported, while stalling can serve as quality control and trigger degradation of aberrant mRNA and peptide. Ribosome profiling has allowed for the genome-wide detection of such pauses and stalls, but due to library-specific biases, these predictions are often unreliable. Here, we take advantage of the deep conservation of protein synthesis machinery, hypothesizing that similar conservation could exist for functionally important locations of ribosome slowdown, here collectively called stall sites. We analyze multiple ribosome profiling datasets from phylogenetically diverse eukaryotes: yeast, fruit fly, zebrafish, mouse and human to identify conserved stall sites. We find thousands of stall sites across multiple species, with the enrichment of proline, glycine and negatively charged amino acids around conserved stalling. Many of the sites are found in RNA processing genes, suggesting that stalling might have a conserved role in RNA metabolism. In summary, our results provide a rich resource for the study of conserved stalling and indicate possible roles of stalling in gene regulation

Herwig 7.1 Release Note

A new release of the Monte Carlo event generator Herwig (version 7.1) is now available. This version introduces a number of improvements, notably: multi-jet merging with the dipole shower at LO and NLO QCD; a new model for soft interactions and diffraction; improvements to mass effects and top decays in the dipole shower, as well as a new tune of the hadronisation parameters.Comment: 7 pages, 7 figures. Herwig is available from https://herwig.hepforge.org

Peptide-Based Coacervate-Core Vesicles with Semipermeable Membranes

Coacervates droplets have long been considered as potential protocells to mimic living cells. However, these droplets lack a membrane and are prone to coalescence, limiting their ability to survive, interact, and organize into higher-order assemblies. This work shows that tyrosine-rich peptide conjugates can undergo liquid–liquid phase separation in a well-defined pH window and transform into stable membrane-enclosed protocells by enzymatic oxidation and cross-linking at the liquid–liquid interface. The oxidation of the tyrosine-rich peptides into dityrosine creates a semipermeable, flexible membrane around the coacervates with tunable thickness, which displays strong intrinsic fluorescence, and stabilizes the coacervate protocells against coalescence. The membranes have an effective molecular weight cut-off of 2.5 kDa, as determined from the partitioning of small dyes and labeled peptides, RNA, and polymers into the membrane-enclosed coacervate protocells. Flicker spectroscopy reveals a membrane bending rigidity of only 0.1kBT, which is substantially lower than phospholipid bilayers despite a larger membrane thickness. Finally, it is shown that enzymes can be stably encapsulated inside the protocells and be supplied with substrates from outside, which opens the way for these membrane-bound compartments to be used as molecularly crowded artificial cells capable of communication or as a vehicle for drug delivery.publishedVersio

Peptide‐Based Coacervate‐Core Vesicles with Semipermeable Membranes

Coacervates droplets have long been considered as potential protocells to mimic living cells. However, these droplets lack a membrane and are prone to coalescence, limiting their ability to survive, interact, and organize into higher-order assemblies. This work shows that tyrosine-rich peptide conjugates can undergo liquid–liquid phase separation in a well-defined pH window and transform into stable membrane-enclosed protocells by enzymatic oxidation and cross-linking at the liquid–liquid interface. The oxidation of the tyrosine-rich peptides into dityrosine creates a semipermeable, flexible membrane around the coacervates with tunable thickness, which displays strong intrinsic fluorescence, and stabilizes the coacervate protocells against coalescence. The membranes have an effective molecular weight cut-off of 2.5 kDa, as determined from the partitioning of small dyes and labeled peptides, RNA, and polymers into the membrane-enclosed coacervate protocells. Flicker spectroscopy reveals a membrane bending rigidity of only 0.1kBT, which is substantially lower than phospholipid bilayers despite a larger membrane thickness. Finally, it is shown that enzymes can be stably encapsulated inside the protocells and be supplied with substrates from outside, which opens the way for these membrane-bound compartments to be used as molecularly crowded artificial cells capable of communication or as a vehicle for drug delivery

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HERWIG 6.4 Release Note

A new release of the Monte Carlo program HERWIG (version 6.4) is now available. The main new features are: spin correlations between the production and decay of heavy fermions, i.e. top quarks, tau leptons and SUSY particles; polarization effects in SUSY production processes in lepton-lepton collisions; an interface to TAUOLA for tau decays; MSSM Higgs processes in lepton-lepton collisions

Herwig++ 2.1 Release Note

A new release of the Monte Carlo program Herwig++ (version 2.1) is now available. This version includes a number of significant improvements including: an eikonal multiple parton-parton scattering model of the underlying event; the inclusion of Beyond the Standard Model (BSM) physics; and a new hadronic decay model tuned to LEP data. This version of the program is now fully ready for the simulation of events in hadron-hadron collisions