Bombesin, vasopressin, and endothelin rapidly stimulate tyrosine phosphorylation in intact Swiss 3T3 cells

The mitogenic neuropeptides bombesin and vasopressin markedly increased tyrosine and serine phosphorylation of multiple substrates in quiescent Swiss 3T3 fibroblasts, including two major bands of Mr 90,000 and 115,000. Tyrosine phosphorylation of these proteins was increased as judged by immunoprecipitation of 32Pi-labeled cells and immunoblotting of unlabeled cells with monoclonal antiphosphotyrosine antibodies, elution with phenyl phosphate, and phospho amino acid analysis. Phosphotyrosyl proteins generated by bombesin and vasopressin did not correspond either by apparent molecular weight or by immunological and biochemical criteria to several known tyrosine kinase substrates, including phospholipase C gamma, the microtubule-associated protein 2 kinase, GTPase-activating protein, or phosphatidylinositol kinase. The effect was rapid (within seconds), concentration dependent, and inhibited by specific receptor antagonists for both bombesin and vasopressin. The endothelin-related peptide, vasoactive intestinal contractor, also elicited a rapid and concentration-dependent tyrosine/serine phosphorylation of a similar set of substrates. These results demonstrate that neuropeptides, acting through receptors linked to GTP-binding proteins, stimulate tyrosine phosphorylation of a common set of substrates in quiescent Swiss 3T3 cells and suggest the existence of an additional signal transduction pathway in neuropeptide-induced mitogenesis

A Repository of Political Party and Interest Group Texts

Work Package 4 of OPTED has created a repository of links to data collections of political text produced by political parties and interest groups (IG), using the definitions and criteria outlined in the first deliverable (D4.1). The repository can be accessed here: https://perma.wzb.eu/opted_wp4_inventory. The inventory consists of two spreadsheets (datasets). One spreadsheet each for political parties and IGs. It contains information about the corpora we identified including temporal, country, and party coverage, accessibility, and usability. The variable text.category informs the user about the text type that can be accessed via the specific corpus, e.g. press releases, manifestos, websites. We regard the repository as a living document that will continue to grow and be updated over the full course of the design phase. The codebook to this repository can be found here: https://perma.wzb.eu/opted_wp4_codebook_inventory. In this report, we provide an overview of our approach to identifying data repositories and the available data we have identified in key areas to date. In the process of creating this repository, we have also identified areas where data has yet to be compiled or is not readily available from online sources

Optimizing an Organized Modularity Measure for Topographic Graph Clustering: a Deterministic Annealing Approach

This paper proposes an organized generalization of Newman and Girvan's modularity measure for graph clustering. Optimized via a deterministic annealing scheme, this measure produces topologically ordered graph clusterings that lead to faithful and readable graph representations based on clustering induced graphs. Topographic graph clustering provides an alternative to more classical solutions in which a standard graph clustering method is applied to build a simpler graph that is then represented with a graph layout algorithm. A comparative study on four real world graphs ranging from 34 to 1 133 vertices shows the interest of the proposed approach with respect to classical solutions and to self-organizing maps for graphs

Structural, electronic, and magnetic properties of CoFeVGe-based compounds: Experiment and theory

We have carried out a combined theoretical and experimental investigation of both stoichiometric and nonstoichiometric CoFeVGe alloys. In particular, we have investigated CoFeVGe, Co1.25Fe0.75VGe, Co0.75Fe1.25VGe, and CoFe0.75VGe bulk alloys. Our first principles calculations suggest that all four alloys show ferromagnetic order, where CoFeVGe, Co1.25Fe0.75VGe, and Co0.75Fe1.25VGe are highly spin polarized with spin polarization values of over 80%. However, the spin polarization value of CoFe0.75VGe is only about 60%. We have synthesized all four samples using arc melting and high-vacuum annealing at 600 °C for 48 hours. The room temperature x-ray diffraction of these samples exhibits a cubic crystal structure with disorder. All the samples show single magnetic transitions at their Curie temperatures, where the Curie temperature and high field (3T) magnetization are 288 K and 42 emu/g; 305 K and 1.5 emu/g; 238 K and 39 emu/g; and 306 K and 35 emu/g for CoFeVGe, Co1.25Fe0.75VGe, Co0.75Fe1.25VGe, and CoFe0.75VGe, respectively

Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes

SummarySomatic mutations in cancer are more frequent in heterochromatic and late-replicating regions of the genome. We report that regional disparities in mutation density are virtually abolished within transcriptionally silent genomic regions of cutaneous squamous cell carcinomas (cSCCs) arising in an XPC−/− background. XPC−/− cells lack global genome nucleotide excision repair (GG-NER), thus establishing differential access of DNA repair machinery within chromatin-rich regions of the genome as the primary cause for the regional disparity. Strikingly, we find that increasing levels of transcription reduce mutation prevalence on both strands of gene bodies embedded within H3K9me3-dense regions, and only to those levels observed in H3K9me3-sparse regions, also in an XPC-dependent manner. Therefore, transcription appears to reduce mutation prevalence specifically by relieving the constraints imposed by chromatin structure on DNA repair. We model this relationship among transcription, chromatin state, and DNA repair, revealing a new, personalized determinant of cancer risk

Elucidating the Role of the Complement Control Protein in Monkeypox Pathogenicity

Monkeypox virus (MPXV) causes a smallpox-like disease in humans. Clinical and epidemiological studies provide evidence of pathogenicity differences between two geographically distinct monkeypox virus clades: the West African and Congo Basin. Genomic analysis of strains from both clades identified a ∼10 kbp deletion in the less virulent West African isolates sequenced to date. One absent open reading frame encodes the monkeypox virus homologue of the complement control protein (CCP). This modulatory protein prevents the initiation of both the classical and alternative pathways of complement activation. In monkeypox virus, CCP, also known as MOPICE, is a ∼24 kDa secretory protein with sequence homology to this superfamily of proteins. Here we investigate CCP expression and its role in monkeypox virulence and pathogenesis. CCP was incorporated into the West African strain and removed from the Congo Basin strain by homologous recombination. CCP expression phenotypes were confirmed for both wild type and recombinant monkeypox viruses and CCP activity was confirmed using a C4b binding assay. To characterize the disease, prairie dogs were intranasally infected and disease progression was monitored for 30 days. Removal of CCP from the Congo Basin strain reduced monkeypox disease morbidity and mortality, but did not significantly decrease viral load. The inclusion of CCP in the West African strain produced changes in disease manifestation, but had no apparent effect on disease-associated mortality. This study identifies CCP as an important immuno-modulatory protein in monkeypox pathogenesis but not solely responsible for the increased virulence seen within the Congo Basin clade of monkeypox virus

Community detection in graphs

The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such clusters, or communities, can be considered as fairly independent compartments of a graph, playing a similar role like, e. g., the tissues or the organs in the human body. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. This problem is very hard and not yet satisfactorily solved, despite the huge effort of a large interdisciplinary community of scientists working on it over the past few years. We will attempt a thorough exposition of the topic, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists, from the discussion of crucial issues like the significance of clustering and how methods should be tested and compared against each other, to the description of applications to real networks.Comment: Review article. 103 pages, 42 figures, 2 tables. Two sections expanded + minor modifications. Three figures + one table + references added. Final version published in Physics Report

Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (, , ) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors. Overall, this large-scale analysis reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining sarcoma therapy and relationships to other cancer types