A5015767793- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Photosynthetic Processes and Mechanisms
- Bacteriophages and microbial interactions
- Plant Stress Responses and Tolerance
- Plant Molecular Biology Research
- Advanced Proteomics Techniques and Applications
- RNA and protein synthesis mechanisms
- Protein Structure and Dynamics
- Bacterial biofilms and quorum sensing
- Salmonella and Campylobacter epidemiology
- Microbial Metabolic Engineering and Bioproduction
- Plant nutrient uptake and metabolism
- Algal biology and biofuel production
- Chemical Reactions and Isotopes
- Antimicrobial Resistance in Staphylococcus
- Computational Drug Discovery Methods
- Ruminant Nutrition and Digestive Physiology
- Protein Kinase Regulation and GTPase Signaling
- Genetic and phenotypic traits in livestock
- Ubiquitin and proteasome pathways
- Bacterial Identification and Susceptibility Testing
- Metal Extraction and Bioleaching
- Click Chemistry and Applications
- Food composition and properties
Technical University of Munich
1991-2025
University of Freiburg
1976
Bacteria are the most abundant and diverse organisms among kingdoms of life. Due to this excessive variance, finding a unified, comprehensive, safe workflow for quantitative bacterial proteomics is challenging. In study, we have systematically evaluated optimized sample preparation, mass spectrometric data acquisition, analysis strategies in proteomics. We investigated performances on six representative species with highly different physiologic properties mimic diversity. The best...
The existence of overlapping genes (OLGs) with significant coding overlaps revolutionizes our understanding genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated in the pathogenic Gram-negative bacterium Pseudomonas aeruginosa. Both OLG pairs show sequence features consistent being transcriptional signals RNA sequencing. Translation both OLGs was confirmed by ribosome...
Mutated KRAS is among the most frequent activating genetic alterations in cancer and drug discovery efforts have led to inhibitors that block its activity. To better understand oncogenic signaling cytostatic effects of drugs, we performed comprehensive dose-dependent proteome-wide target deconvolution, pathway engagement protein expression characterization KRAS, MEK, ERK, SHP2 SOS1 pancreatic (KRAS G12C, G12D) lung G12C) cells. Analysis resulting 687,954 dose-response curves available online...
Transport Protein Particle II (TRAPPII) is essential for exocytosis, endocytosis, protein sorting and cytokinesis. In spite of a considerable understanding its biological role, little information known about Arabidopsis TRAPPII complex topology molecular function. this study, independent proteomic approaches initiated with TRAPP components or Rab-A GTPase variants converge on the complex. We show that genome encodes full complement 13 TRAPPC subunits, including four previously unidentified...
The ability of certain Pseudomonas ( P. ) species to grow or persist in anoxic habitats by either denitrification, acetate fermentation, arginine fermentation has been described several studies as a special property. Previously, we had isolated strains belonging the lundensis , weihenstephanensis and fragi from modified atmosphere packaged (MAP) minced beef further proved their anaerobic growth vitro on agar plates. This follow-up study investigated two per respective situ inoculated chicken...
Lysine deacetylase inhibitors (KDACis) are approved drugs for cutaneous T cell lymphoma (CTCL), peripheral (PTCL), and multiple myeloma, but many aspects of their cellular mechanism action (MoA) substantial toxicity not well understood. To shed more light on how KDACis elicit responses, we systematically measured dose-dependent changes in acetylation, phosphorylation, protein expression response to 21 clinical pre-clinical KDACis. The resulting 862,000 dose-response curves revealed,...
Abstract With climate change, droughts are expected to be more frequent and severe, severely impacting plant biomass quality. Here, we show that overexpressing the Arabidopsis gene AtFtsHi3 ( FtsHi3OE) enhances drought‐tolerant phenotypes without compromising growth. encodes a chloroplast envelope pseudo‐protease; knock‐down mutants ftshi3‐1 ) found drought tolerant but exhibit stunted Altered expression therefore leads tolerance, while only diminished of this growth retardation. To...
Plants often adapt to adverse or stress conditions via differential growth. The trans-Golgi network (TGN) has been implicated in responses, but it is not clear what capacity mediates adaptive growth decisions. In this study, we assess the role of TGN responses by exploring previously identified interactome Transport Protein Particle II (TRAPPII) complex required for structure and function. We physical genetic interactions between AtTRAPPII shaggy-like kinases (GSK3/AtSKs) provided vitro vivo...
Finding the targets of natural products is key importance in both chemical biology and drug discovery, deconvolution cofactor interactomes contributes to functional annotation proteome. Identifying proteins that underlie compound activity phenotypic screens helps validate respective and, potentially, expand druggable Here, we present a generally applicable protocol for photoactivated immobilization unmodified microgram quantities on diazirine-decorated beads their use systematic...
The biofilm associated protein (Bap) is recognised as the essential component for formation in Staphylococcus aureus V329 and has been predicted important other species well. Although Bap orthologs are also present most S. xylosus strains, their contribution to not yet demonstrated. In this study, different experimental approaches were used elucidate effect of on motif structure two biofilm-forming strains TMW 2.1023 2.1523 was compared V329. We found that despite an identical structural...
Abstract Campylobacter jejuni and Arcobacter butzleri are microaerobic food-borne human gastrointestinal pathogens that mainly cause diarrheal disease. These related species of the Campylobacteria class face variable atmospheric environments during infection transmission, ranging from nearly anaerobic to aerobic conditions. Consequently, their lifestyles require both need adjust metabolism respiration changing oxygen concentrations colonization sites. Our studies revealed C. A. lacking a...
Bottom-up proteomics in synergy with big data science has significantly advanced microbiological research. Comprehensive proteome profiling is pivotal advancing our knowledge of bacteria and their interactions the environment, other organisms, human health. Although many proteomic methods exist (sample preparation, mass-spectrometric acquisition, analysis), most have only been validated on eukaryotic samples. However, possess very distinctive characteristics. For example, rigid cell walls...
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Abstract Bifidobacterium species and strains are key members of the gut microbiota, appearing soon after birth persisting into adulthood. Resistant starch is an important dietary substrate for adult-associated bifidobacteria, where its fermentation supports host health. However, little known about how different structures interact with bifidobacteria across various ages ecological niches. To address this, we carried out detailed growth kinetics screening reference unique isolates from...
Abstract Given sustainability and scalability concerns of using sugar feedstocks for microbial bioproduction bulk chemicals, widening the feedstock range cell factories is high interest. Methanol a one-carbon alcohol that stands out as an alternative it electron-rich, water-miscible can be produced from several renewable resources. Bioconversion methanol into products under thermophilic conditions (>50°C) could highly advantageous industrial biotechnology. However, natural methylotrophic...
Quantitative mass spectrometry has revolutionized proteomics by enabling simultaneous quantification of thousands proteins. Pooling patient-derived data from multiple institutions enhances statistical power but raises significant privacy concerns. Here we introduce FedProt, the first privacy-preserving tool for collaborative differential protein abundance analysis distributed data, which utilizes federated learning and additive secret sharing. In absence a multicenter dataset evaluation,...
Abstract The existence of overlapping genes (OLGs) with significant coding overlaps revolutionises our understanding genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated in the medically important Gram-negative bacterium Pseudomonas aeruginosa . Both OLG pairs show sequence features consistent being transcriptional signals RNA sequencing data. Translation both OLGs was...
Modified atmosphere packaging (MAP) is a common strategy to selectively prevent the growth of certain species meat spoiling bacteria. This study aimed determine impact high oxygen MAP (70% O2, 30% CO2, red and white meats) oxygen-free N2, also seafood) on preventing photobacteria meat. Growth Photobacterium carnosum P. phosphoreum was monitored in simulation media under different gas mixtures nitrogen, oxygen, carbon dioxide, samples were taken during exponential for comparative proteomic...