A5071402164- Immune Cell Function and Interaction
- T-cell and B-cell Immunology
- Cancer Immunotherapy and Biomarkers
- Genetics, Aging, and Longevity in Model Organisms
- Plant Molecular Biology Research
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- Plant Reproductive Biology
- Acute Myeloid Leukemia Research
- Metabolomics and Mass Spectrometry Studies
- Diabetes and associated disorders
- Single-cell and spatial transcriptomics
- Light effects on plants
- Cytomegalovirus and herpesvirus research
- Laser-Matter Interactions and Applications
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- IL-33, ST2, and ILC Pathways
- Immune responses and vaccinations
- Ion-surface interactions and analysis
- Polysaccharides and Plant Cell Walls
- 3D Printing in Biomedical Research
- Immunodeficiency and Autoimmune Disorders
- Inflammatory Biomarkers in Disease Prognosis
- Immunotherapy and Immune Responses
University Hospital of Basel
2016-2023
University of Basel
2019-2023
SIB Swiss Institute of Bioinformatics
2019-2023
Helmholtz Zentrum München
2022
Helmholtz Centre for Environmental Research
2020
Imperial College London
2009-2019
Roche (Switzerland)
2019
Klinikum Braunschweig
2019
University Hospital of Zurich
2019
Charlottesville Medical Research
2019
We elucidate the detailed effects of gut microbial depletion on bile acid sub-metabolome multiple body compartments (liver, kidney, heart, and blood plasma) in rats. use a targeted ultra-performance liquid chromatography with time flight mass-spectrometry assay to characterize differential primary secondary profiles each tissue show major increase proportion taurine-conjugated acids germ-free (GF) antibiotic (streptomycin/penicillin)-treated Although conjugated dominate hepatic profile (97.0...
Trichome and root hair patterning are governed by a conserved cassette of bHLH MYB factors, the WD40 protein TTG1, six single-repeat R3 factors that thought to counteract them. In this work we focus on factor ETC3 show its major role is in regulation trichome density redundant manner. Diversification gene has occurred at promoter level, as etc3 mutants can be rescued expressing under control TRY or CPC promoter. movement was detected between epidermal cells well epidermis underlying tissues....
Trichome patterning in Arabidopsis serves as a model system to study how single cells are selected within field of initially equivalent cells. Current models explain this pattern by an activator-inhibitor feedback loop. Here, we report that also newly discovered mechanism is involved which governed the removal trichome-promoting factor TRANSPARENT TESTA GLABRA1 (TTG1) from non-trichome We demonstrate clonal analysis and misexpression studies TTG1 can act non-cell-autonomously microinjection...
Myeloproliferative neoplasm (MPN) patients frequently show co-occurrence of JAK2-V617F and mutations in epigenetic regulator genes, including EZH2. In this study, we that loss Ezh2 hematopoietic cells contribute synergistically to the development MPN. The MPN phenotype induced by was accentuated JAK2-V617F;Ezh2−/− mice, resulting very high platelet neutrophil counts, more advanced myelofibrosis, reduced survival. These mice also displayed expansion stem cell progenitor compartments a shift...
Interferon-driven inflammation in chronic viral infection blocks generation of sustained B cell responses. See related Research Articles by Moseman et al. and Sammicheli a Focus Laidlaw
CD4+ memory T cells play an important role in protective immunity and are a key target vaccine development. Many studies have focused on central (Tcm) cells, whereas the existence functional significance of long-lived follicular helper (Tfh) controversial. Here, we show that Tfh highly susceptible to NAD-induced cell death (NICD) during isolation from tissues, leading their underrepresentation prior studies. NICD blockade reveals persistence abundant with high expression hallmark markers at...
Single-nucleotide polymorphisms in the gene encoding G protein-coupled receptor 35 (GPR35) are associated with increased risk of inflammatory bowel disease. However, mechanisms by which GPR35 modulates intestinal immune homeostasis remain undefined. Here, integrating zebrafish and mouse experimental models, we demonstrate that Gpr35 expression is microbiota dependent enhanced upon inflammation. Moreover, murine GPR35+ colonic macrophages characterized production pro-inflammatory cytokines....
Obesity promotes diverse pathologies, including atherosclerosis and dementia, which frequently involve vascular defects endothelial cell (EC) dysfunction. Each organ has distinct EC subtypes, but whether ECs are differentially affected by obesity is unknown. Here we use single-cell RNA sequencing to analyze transcriptomes of ~375,000 from seven organs in male mice at progressive stages identify organ-specific vulnerabilities. We find that deregulates gene expression networks, lipid handling,...
T cell factor 1 (Tcf-1) expressing CD8+ cells exhibit stem-like self-renewing capacity, rendering them key for immune defense against chronic viral infection and cancer. Yet, the signals that promote formation maintenance of these (CD8+SL) remain poorly defined.Studying differentiation in mice with infection, we identified alarmin interleukin-33 (IL-33) as pivotal expansion functioning CD8+SL well virus control. IL-33 receptor (ST2)-deficient exhibited biased end premature loss Tcf-1....
Cellular processes are controlled by gene-regulatory networks. Several computational methods currently used to learn the structure of networks from data. This study focusses on time series gene expression and knock-out data in order identify underlying network structure. We compare performance different reconstruction using synthetic generated an ensemble reference Data requirements as well optimal experiments for investigated. Additionally, impact prior knowledge effect unobserved cellular...
The nematode Caenorhabditis elegans is widely used as a model organism in many areas of the life sciences. Metabolite profiling (metabolomics/metabonomics) powerful means assigning phenotypes to experimentally perturbed C. samples (e.g., mutants, RNAi, or chemical treatments). Tissue extraction key step, and high-quality reproducible extractions are essential success metabolomics studies. We have performed an extensive comparison different tissue techniques with elegans, comparing two...
The transcription factor POU5f1/OCT4 controls pluripotency in mammalian ES cells, but little is known about its functions the early embryo. We used time‐resolved transcriptome analysis of zebrafish pou5f1 MZ spg mutant embryos to identify genes regulated by Pou5f1. Comparison systems defines evolutionary conserved Pou5f1 targets. Time‐series data reveal many targets with delayed or advanced onset expression. two Pou5f1‐dependent mechanisms controlling developmental timing. First, several are...
Article2 September 2008Open Access A competitive complex formation mechanism underlies trichome patterning on Arabidopsis leaves Simona Digiuni Department of Botany III, Botanical Institute, University Cologne, Germany Search for more papers by this author Swen Schellmann Florian Geier Mathematics and Physics, Freiburg, Biology, Center Biological Systems Analysis, Bettina Greese Martina Pesch Katja Wester Burcu Dartan Valerie Mach Bhylahalli Purushottam Srinivas Jens Timmer Freiburg...
The genome of the nematode Caenorhabditis elegans encodes for two multifunctional metal binding metallothioneins (MTs), CeMT-1 and CeMT-2. Here we applied qPCR to identify a transcriptional up-regulation following exposure free radical generators (ROS) paraquat or hydrogen peroxide, trend that was confirmed with Pmtl::GFP expressing alleles. deletion MT loci resulted in an elevation vivo levels peroxide ROS caused reduction total egg production, growth life span wild type nematodes, effects...
We present a fully integrated droplet-based microfluidic platform for the high-throughput assessment of photodynamic therapy photosensitizer (PDT) efficacy on Escherichia coli. The described is able to controllably encapsulate cells and within pL-volume droplets, incubate droplets over course several days, add predetermined concentrations viability assay agents, expose varying doses electromagnetic radiation, detect both live dead online score cell viability. after encapsulation incubation...
Abstract Purpose: PD-(L)1–blocking antibodies have clinical activity in metastatic non–small cell lung cancer (NSCLC) and mediate durable tumor remissions. However, the majority of patients are resistant to PD-(L)1 blockade. Understanding mechanisms primary resistance may allow prediction response identification new targetable pathways. Experimental Design: Peripheral blood mononuclear cells were collected from 35 with NSCLC receiving nivolumab monotherapy. Cellular changes, cytokine levels,...
Arrhythmogenic cardiomyopathy (ACM) is characterized by progressive loss of cardiomyocytes with fibrofatty tissue replacement, systolic dysfunction, and life-threatening arrhythmias. A substantial proportion ACM caused mutations in genes the desmosomal cell-cell adhesion complex, but underlying mechanisms are not well understood. In current study, we investigated relevance defective for development progression.We mutated binding site DSG2 (desmoglein-2), a crucial molecule cardiomyocytes....
Nuclear magnetic resonance (NMR) spectroscopy is widely used as an analytical platform for metabolomics. Many studies make use of 1D spectra, which have the advantages relative simplicity and rapid acquisition times. The spectral data can then be analyzed either with a chemometric workflow or by initial deconvolution fitting step to generate list identified metabolites associated sample concentrations. Various software tools exist simplify process, but at least this still requires degree...
To adapt the timing of processes regulated by circadian clock to seasonally varying photoperiods, phase relation between and dusk or dawn ("phase entrainment") must be tightly adjusted. The authors use a mathematical model molecular mammalian oscillator investigate influence free-running period (tau) shape PRC on entrainment. They find that phase-dependent sensitivity ("gating") light-induced gene transcription enables constant under different photoperiods. Depending freerunning tau shaping...
Plants maintain pools of totipotent stem cells throughout their entire life. These are embedded within specialized tissues called meristems, which form the growing points organism. The shoot apical meristem reference plant Arabidopsis thaliana is subdivided into several distinct domains, execute diverse biological functions, such as tissue organization, cell-proliferation and differentiation. number required for growth organ formation changes over course a plants life, while structure...
We present a passive microfluidic strategy for sorting adult C. elegans nematodes on the basis of age and size. The separation mechanism takes advantage phenotypic differences between 'adult' 'juvenile' organisms their behaviour in architectures. In brief, device allows worms to sort themselves manner.
To investigate molecular changes in multiple sclerosis (MS) normal-appearing cortical gray matter (NAGM).We performed a whole-genome gene expression microarray analysis of human brain autopsy tissues from 64 MS NAGM samples and 42 control samples. We further examined our cases by HLA genotyping immunohistochemical immunofluorescent all tissues.HLA-DRB1 is the transcript with highest bimodal distribution among cases. Genotyping revealed that every case MS-associated HLA-DR15 haplotype also...
Digit loss/reductions are evolutionary adaptations in cursorial mammals such as pigs. To gain mechanistic insight into these processes, we performed a comparative molecular analysis of limb development mouse and pig embryos, which revealed loss anterior-posterior polarity during distal progression bud development. These alterations buds paralleled by changes the mesenchymal response to Sonic hedgehog (SHH) signaling, is altered upstream reduction Fgf8 expression ectoderm that overlaps...