The role of Dickkopf-3 in tissue mediated immune modulation

The immune system protects our organism from harmful environmental insults. Pathogens induce innate and adaptive immune responses that resolve infection and clear damaged cells. A tight balance between efficient elimination of the initial insult and the containment of the immune response, assures protection of the organism as well as the preservation of organ integrity. Disregulation of this system can lead to devastating effects like tissue damage and organ failure caused by excessive inflammation. Tissue components play a pivotal role in the regulation of immune responses. In order to develop novel therapeutic strategies for the treatment of inflammatory diseases, their properties have to be incorporated. Hence, a detailed understanding of mechanisms by which tissue cells influence immune responses is indispensable. Recently, our lab identified Dickkopf-3 (Dkk3) as an immune modulator mainly expressed by tissue cells. Thus we aimed to uncover the contribution of Dkk3 to tissue mediated immune modulation during inflammation. With the help of a transgenic mouse model we investigated how antigen-presenting keratinocytes in the inflamed skin modulate T cell reactivity. In these mice, keratinocytes present a myelin basic protein (MBP) peptide only upon skin inflammation. In the absence of systemic MBP immunization acute skin inflammation resulted in keratinocyte-mediated activation of MBP-specific CD4+ T cells that were encephalitogenic. However, chronic skin inflammation limited the encephalitogenic potential of systemically primed MBP-specific T cells. In this setting Dickkopf-3 was indispensable for the limitation of CD4 T cell reactivity. We successfully generated a transgenic Dkk3 reporter mouse that reliably indicates sites of Dkk3 expression. Furthermore, in vitro and in vivo studies identified interferon-γ (IFNγ) as a potent regulator of Dkk3 expression in tissue cell. Finally, we found that Dkk3 promotes the development of renal fibrosis in 2 different mouse models, indicated by decreased severity of fibrosis in Dkk3 deficient mice. Furthermore, we observed that Dkk3 expression is induced in tubular epithelial cells in the course of fibrosis development. Less fibrosis in Dkk3 deficient mice was accompanied by elevated levels of pro-inflammatory cytokines and increased T cell infiltration in the respective kidneys. Additionally, we observed an altered polarization of infiltrating CD4 T cells towards a Th1/Treg phenotype in dkk3-/- kidneys, which came along with decreased expression of Wnt target genes in these cells. In conclusion, Dkk3 contributes to tissue mediated immune modulation by regulation of T cell responses

Ultra-thin Topological Insulator Bi2Se3 Nanoribbons Exfoliated by Atomic Force Microscopy

Ultra-thin topological insulator nanostructures, in which coupling between top and bottom surface states takes place, are of great intellectual and practical importance. Due to the weak Van der Waals interaction between adjacent quintuple layers (QLs), the layered bismuth selenide (Bi2Se3), a single Dirac-cone topological insulator with a large bulk gap, can be exfoliated down to a few QLs. In this paper, we report the first controlled mechanical exfoliation of Bi2Se3 nanoribbons (> 50 QLs) by an atomic force microscope (AFM) tip down to a single QL. Microwave impedance microscopy is employed to map out the local conductivity of such ultra-thin nanoribbons, showing drastic difference in sheet resistance between 1~2 QLs and 4~5 QLs. Transport measurement carried out on an exfoliated (\leq 5 QLs) Bi2Se3 device shows non-metallic temperature dependence of resistance, in sharp contrast to the metallic behavior seen in thick (> 50 QLs) ribbons. These AFM-exfoliated thin nanoribbons afford interesting candidates for studying the transition from quantum spin Hall surface to edge states

miRA: adaptable novel miRNA identification in plants using small RNA sequencing data

BACKGROUND: MicroRNAs (miRNAs) are short regulatory RNAs derived from longer precursor RNAs. miRNA biogenesis has been studied in animals and plants, recently elucidating more complex aspects, such as non-conserved, species-specific, and heterogeneous miRNA precursor populations. Small RNA sequencing data can help in computationally identifying genomic loci of miRNA precursors. The challenge is to predict a valid miRNA precursor from inhomogeneous read coverage from a complex RNA library: while the mature miRNA typically produces many sequence reads, the remaining part of the precursor is covered very sparsely. As recent results suggest, alternative miRNA biogenesis pathways may lead to a more diverse miRNA precursor population than previously assumed. In plants, the latter manifests itself in e.g. complex secondary structures and expression from multiple loci within precursors. Current miRNA identification algorithms often depend on already existing gene annotation, and/or make use of specific miRNA precursor features such as precursor lengths, secondary structures etc. Consequently and in view of the emerging new understanding of a more complex miRNA biogenesis in plants, current tools may fail to characterise organism-specific and heterogeneous miRNA populations. RESULTS: miRA is a new tool to identify miRNA precursors in plants, allowing for heterogeneous and complex precursor populations. miRA requires small RNA sequencing data and a corresponding reference genome, and evaluates precursor secondary structures and precursor processing accuracy; key parameters can be adapted based on the specific organism under investigation. We show that miRA outperforms the currently best plant miRNA prediction tools both in sensitivity and specificity, for data involving Arabidopsis thaliana and the Volvocine algae Chlamydomonas reinhardtii; the latter organism has been shown to exhibit a heterogeneous and complex precursor population with little cross-species miRNA sequence conservation, and therefore constitutes an ideal model organism. Furthermore we identify novel miRNAs in the Chlamydomonas-related organism Volvox carteri. CONCLUSIONS: We propose miRA, a new plant miRNA identification tool that is well adapted to complex precursor populations. miRA is particularly suited for organisms with no existing miRNA annotation, or without a known related organism with well characterized miRNAs. Moreover, miRA has proven its ability to identify species-specific miRNAs. miRA is flexible in its parameter settings, and produces user-friendly output files in various formats (pdf, csv, genome-browser-suitable annotation files, etc.). It is freely available at https://github.com/mhuttner/miRA .The authors acknowledge funding from the Deutsche Forschungsgemeinschaft (SFB 960), the Bavarian Genome Research Network (BayGene), and the Bavarian Biosystems Network (BioSysNet)

MATSim-T : Architecture and Simulation Times

Micro-simulations for transport planning are becoming increasingly important in traffic simulation, traffic analysis, and traffic forecasting. In the last decades the shift from using typically aggregated data to more detailed, individual based, complex data (e.g. GPS tracking) andthe continuously growing computer performance on fixed price level leads to the possibility of using microscopic models for large scale planning regions. This chapter presents such a micro-simulation. The work is part of the research project MATSim (Multi Agent Transport Simulation, http://matsim.org). In the chapter here the focus lies on design and implementation issues as well as on computational performance of different parts of the system. Based on a study of Swiss daily traffic – ca. 2.3 million individuals using motorized individual transport producing about 7.1 million trips, assigned to a Swiss network model with about 60,000 links, simulated and optimized completely time-dynamic for a complete workday – it is shown that the system is able to generate those traffic patterns in about 36 hours computation time

Antagonisms in the EU’s neighbourhood The EU, Russia, Turkey, Iran and Saudi Arabia struggle for influence in their common neighbourhood. Bertelsmann Stiftung Strategies for the EU neighbourhood #1

In pursuing its objective of building a ring of stable states to the east and south of its borders from Belarus to Morocco, the European Union must recognise that the room for manoeuvre in its neighbourhood has become narrower. Four states in particular are playing an ever more active role: Russia, Turkey, Iran and Saudi Arabia. They are increasingly influencing the EU's immediate neighbours, many of whom are also their immediate geographical neighbours. From a European perspective, these four large countries can also be described as "neighbours of the EU's neighbours" and "key states" in relation to the European neighbourhoo

Implementation of paediatric precision oncology into clinical practice: The Individualized Therapies for Children with cancer program 'iTHER'

iTHER is a Dutch prospective national precision oncology program aiming to define tumour molecular profiles in children and adolescents with primary very high-risk, relapsed, or refractory paediatric tumours. Between April 2017 and April 2021, 302 samples from 253 patients were included. Comprehensive molecular profiling including low-coverage whole genome sequencing (lcWGS), whole exome sequencing (WES), RNA sequencing (RNA-seq), Affymetrix, and/or 850k methylation profiling was successfully performed for 226 samples with at least 20% tumour content. Germline pathogenic variants were identified in 16% of patients (35/219), of which 22 variants were judged causative for a cancer predisposition syndrome. At least one somatic alteration was detected in 204 (90.3%), and 185 (81.9%) were considered druggable, with clinical priority very high (6.1%), high (21.3%), moderate (26.0%), intermediate (36.1%), and borderline (10.5%) priority. iTHER led to revision or refinement of diagnosis in 8 patients (3.5%). Temporal heterogeneity was observed in paired samples of 15 patients, indicating the value of sequential analyses. Of 137 patients with follow-up beyond twelve months, 21 molecularly matched treatments were applied in 19 patients (13.9%), with clinical benefit in few. Most relevant barriers to not applying targeted therapies included poor performance status, as well as limited access to drugs within clinical trial. iTHER demonstrates the feasibility of comprehensive molecular profiling across all ages, tumour types and stages in paediatric cancers, informing of diagnostic, prognostic, and targetable alterations as well as reportable germline variants. Therefore, WES and RNA-seq is nowadays standard clinical care at the Princess Máxima Center for all children with cancer, including patients at primary diagnosis. Improved access to innovative treatments within biology-driven combination trials is required to ultimately improve survival. Keywords: Adolescent; Cancer; Child; Hereditary; Molecular biology; Molecular targeted therapy; Next-generation sequencing; Precision medicin