A5041718313- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Bacterial biofilms and quorum sensing
- Antibiotic Resistance in Bacteria
- Cancer Cells and Metastasis
- Bacteriophages and microbial interactions
- Legume Nitrogen Fixing Symbiosis
- Plant-Microbe Interactions and Immunity
- Cellular Mechanics and Interactions
- Probiotics and Fermented Foods
- Listeria monocytogenes in Food Safety
- Bacterial Identification and Susceptibility Testing
- Bacterial Genetics and Biotechnology
- Identification and Quantification in Food
- Salivary Gland Tumors Diagnosis and Treatment
- Plant Pathogenic Bacteria Studies
- Single-cell and spatial transcriptomics
- Plant responses to water stress
- Endoplasmic Reticulum Stress and Disease
- Heterotopic Ossification and Related Conditions
- Actinomycetales infections and treatment
- Microbial Inactivation Methods
- Radiomics and Machine Learning in Medical Imaging
- 3D Printing in Biomedical Research
- Bartonella species infections research
Fraunhofer Institute for Toxicology and Experimental Medicine
2021-2024
SIB Swiss Institute of Bioinformatics
2015-2023
Agroscope
2015-2023
ETH Zurich
2019-2020
Department of Medical Sciences
2019
École Polytechnique Fédérale de Lausanne
2017
Wageningen University & Research
2017
International Rice Research Institute
2013
The plant kingdom represents a prominent biodiversity island for microbes that associate with the below- or aboveground organs of vegetal species. Both root and leaf represent interfaces where dynamic biological interactions influence life. Beside well-studied communication strategies based on soluble compounds protein effectors, bacteria were recently shown to interact both host plants other microbial species through emissions volatile organic (VOCs). Focusing potato late blight-causing...
Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire completely sequenced prokaryotic genomes. However, large discrepancies among number CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction spurious ORFs represent serious limitations. Our strategy toward accurate complete genome consolidates from multiple reference ab initio gene prediction algorithms...
Although complete genome sequences hold particular value for an accurate description of core genomes, the identification strain-specific genes, and as optimal basis functional genomics studies, they are still largely underrepresented in public repositories. Based on assessment assembly complexity all lactobacilli, we used Pacific Biosciences' long read technology to sequence de novo assemble genomes three Lactobacillus helveticus starter strains, raising number completely sequenced strains...
For plants, the advantages of associating with beneficial bacteria include plant growth promotion, reduction abiotic and biotic stresses enhanced protection against various pests diseases. Beneficial rightly equipped for successful colonization showing antagonistic activity towards pathogens seem to be actively recruited by plants. To gain more insights into genetic determinants responsible activities, we first sequenced de novo assembled complete genomes nine Pseudomonas strains that had...
Abstract Pseudomonas aeruginosa MPAO1 is the parental strain of widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and biofilm-associated antibiotic resistance. Our employs genomics-driven workflow assemble complete genome, unique conserved by comparative genomics with PAO1 reference missed within existing assemblies proteogenomics. Among over 200 genes, identified six general...
Abstract Heterotopic ossification (HO) represents a common problem after tendon injury with no effective treatment yet being developed. Tenomodulin ( Tnmd ), the best-known mature marker for lineage cells, has important effects in tissue aging and function. We have reported that loss of leads to inferior early repair characterized by fibrovascular scaring therefore hypothesized its lack will persistently cause deficient during later stages. knockout −/− ) wild-type (WT) animals were...
Aureobasidium pullulans is an extremotolerant, cosmopolitan yeast-like fungus that successfully colonises vastly different ecological niches. The species widely used in biotechnology and applied as a commercial biocontrol agent against postharvest diseases fireblight. However, the exact mechanisms are responsible for its antagonistic activity diverse plant pathogens not known at molecular level. Thus, it difficult to optimise improve applications of this species. As foundation elucidating...
Small open reading frame encoded proteins (SEPs) gained increasing interest during the last few years because of their broad range important functions in both prokaryotes and eukaryotes. In bacteria, signaling, virulence, regulation enzyme activities have been associated with SEPs. Nonetheless, number SEPs detected large-scale proteome studies is often low as classical methods are biased toward identification larger proteins. Here, we present a workflow that allows enhanced small compared to...
Abstract The analysis of volatiles from bacterial cultures revealed long‐chain aliphatic nitriles, a new class natural products. Such nitriles are produced by both Gram‐positive Micromonospora echinospora and Gram‐negative Pseudomonas veronii bacteria, although the structures differ. A variable sequence chain elongation dehydration in fatty acid biosynthesis leads to either unbranched saturated or unsaturated with an ω−7 double bond, such as ( Z )‐11‐octadecenenitrile, methyl‐branched bond...
The adaptation of rhizobia from the free-living state in soil to endosymbiotic comprises several physiological changes order cope with extremely low oxygen availability (microoxia) within nodules. To uncover cellular functions required for bacterial microoxia directly at protein level, we applied a systems biology approach on key rhizobial model and soybean endosymbiont Bradyrhizobium diazoefficiens USDA 110 (formerly B. japonicum 110). As first step, complete genome 110spc4, strain used...
Solid cancers frequently relapse with distant metastasis, despite local and systemic treatment. Cellular dormancy has been identified as an important mechanism underlying drug resistance enabling late relapse. Therefore, from invisible, minimal residual cancer of seemingly disease-free patients call for in vitro models dormant cells suited discovery. Here, we explore dormancy-inducing 3D engineered matrices, which generate mechanical confinement induce growth arrest survival against...
Listeria monocytogenes is an opportunistic foodborne pathogen responsible for listeriosis, a potentially fatal disease. Many different strains and serotypes exist, but proteogenomic resource that bridges the gap in our molecular understanding of relationships between genotypes phenotypes via proteotypes still missing. Here, we devised next-generation proteogenomics strategy enables community to rapidly proteotype relate this information back genotype. Based on sequencing de novo assembly two...
Bacterial ribosome-dependent attenuators are widespread posttranscriptional regulators. They harbor small upstream open reading frames (uORFs) encoding leader peptides, for which no functions in
Pseudomonas aeruginosa is an opportunistic pathogen of considerable medical importance, owing to its pronounced antibiotic tolerance and association with cystic fibrosis other life-threatening diseases. The aim this study was highlight the genes responsible for P. biofilm antibiotics thereby identify potential new targets development drugs against biofilm-related infections. By developing a novel screening approach utilizing public transposon insertion library, several biofilm-relevant were...
Abstract Introduction: Liquid biopsy enables minimally invasive molecular profiling of systemic cancer for diagnosis, therapy selection and longitudinal monitoring minimal residual disease. Cell-based liquid methods are particularly well suited to examine the extent genetic heterogeneity clonal diversity among metastatic cells, which believed be major determinants therapeutic failure. However, isolation circulating tumor cells (CTCs) from body fluids is challenging due methodological...
Abstract Liquid biopsy provides opportunities to guide therapy decisions using biomarkers such as circulating tumor cells (CTCs) even years after the primary resection. For this, novel methods permitting genomic profiling of CTCs are needed characterize systemic cancer spread and identify clinically targetable alterations. Hence, we developed an assay based on FDA-approved MSK-IMPACT® analyze genomes single-cells. We present a series benchmarking experiments well-characterized cell lines...
Abstract Molecular profiling of rare cancer cells derived from liquid biopsy holds promise to monitor systemic progression and guide personalized therapy interventions. However, this necessitates reliable comprehensive samples at the single cell level requires whole genome amplification (WGA), which adds errors bias common sequencing errors. Therefore, we established a single-cell mutation calling workflow that can identify clinically actionable somatic mutations in DNA with high sensitivity...
While cell‐free liquid biopsy (cfLB) approaches provide simple and inexpensive disease monitoring, cell‐based (cLB) may enable additional molecular genetic assessment of systemic heterogeneity preclinical model development. We investigated 71 blood samples 62 patients with various advanced cancer types subjected enriched circulating tumor cells (CTCs) to organoid culture conditions. CTC‐derived tumoroid models were characterized by DNA/RNA sequencing immunohistochemistry, as well functional...
Abstract Pseudomonas aeruginosa MPAO1 is the parental strain of widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and antibiotic resistance. Our employs genomics-driven workflow assemble complete genome, unique conserved by comparative genomics with PAO1 reference missed proteogenomics. Among over 200 genes, identified six general essential that were overlooked when mapping public...
Abstract Resected tumors frequently relapse with distant metastasis, despite systemic treatment. Cellular dormancy has been identified as an important mechanism underlying such drug resistance enabling late relapse. Nonetheless, hurdles associated detection and isolation of disseminated cancer cells (DCCs) in disease-free patients urge the need for vitro models dormant suited discovery. Here, we explore dormancy-inducing 3D-engineered matrices, which generate mechanical confinement induce...
Abstract Langkettige aliphatische Nitrile, eine neue Naturstoffklasse, wurden durch Analyse flüchtiger Verbindungen aus Bakterienkulturen gefunden. Diese Nitrile werden von Gram‐positiven Micromonospora echinospora und Gram‐negativen Pseudomonas veronii produziert, jedoch mit unterschiedlichen Strukturmerkmalen. Eine flexible Abfolge Kettenverlängerungen Dehydratisierung in der Fettsäurebiosynthese führt zu unverzweigten gesättigten Nitrilen entsprechenden ungesättigten ω−7‐Doppelbindung,...
Actinomyces succiniciruminis strain Am4T, isolated from cow rumen fluid, can metabolize a range of substrates including complex carbohydrates to organic acids. Here, we report 3.33-Mbp draft genome succiniciruminis.