- Tuberculosis Research and Epidemiology
- RNA and protein synthesis mechanisms
- Advanced Proteomics Techniques and Applications
- Microbial Community Ecology and Physiology
- Mycobacterium research and diagnosis
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Protist diversity and phylogeny
- Vibrio bacteria research studies
- Bacterial Genetics and Biotechnology
- Fungal and yeast genetics research
- Bioinformatics and Genomic Networks
- Planarian Biology and Electrostimulation
- Marine Ecology and Invasive Species
- Plant and fungal interactions
- CRISPR and Genetic Engineering
- Biochemical and Molecular Research
- Plant-based Medicinal Research
- Gene expression and cancer classification
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Biosensors and Analytical Detection
- Peptidase Inhibition and Analysis
- Bacteriophages and microbial interactions
ETH Zurich
2015-2025
Swiss Federal Institute of Aquatic Science and Technology
2022-2025
University of California, Los Angeles
2016-2024
University of Southern California
2024
IIT@MIT
2024
Systems Dynamics (United States)
2024
Howard Hughes Medical Institute
2021-2022
QB3
2022
École Polytechnique Fédérale de Lausanne
2022
Life Science Zurich
2013-2015
Abstract Mass spectrometry is the method of choice for deep and reliable exploration (human) proteome. Targeted mass reliably detects quantifies pre-determined sets proteins in a complex biological matrix used studies that rely on quantitatively accurate reproducible measurement across multiple samples. It requires one-time, priori generation specific assay each targeted protein. SWATH-MS spectrometric combines data-independent acquisition (DIA) data analysis vastly extends throughput can be...
Cell-surface proteins are of great biomedical importance, as demonstrated by the fact that 66% approved human drugs listed in DrugBank database target a cell-surface protein. Despite this relevance, there has been no comprehensive assessment surfaceome, and only fraction predicted 5,000 transmembrane have shown to be located at plasma membrane. To enable analysis we developed surfaceome predictor SURFY, based on machine learning. As training set, used experimentally verified high-confidence...
Deciphering physiological changes that mediate transition of Mycobacterium tuberculosis between replicating and nonreplicating states is essential to understanding how the pathogen can persist in an individual host for decades. We have combined RNA sequencing (RNA-seq) 5′ triphosphate-enriched libraries with regular RNA-seq characterize architecture expression M. promoters. identified over 4,000 transcriptional start sites (TSSs). Strikingly, 26% genes a primary TSS, site initiation...
A key barrier to the realization of personalized medicine for cancer is identification biomarkers. Here we describe a two-stage strategy discovery serum biomarker signatures corresponding specific cancer-causing mutations and its application prostate (PCa) in context commonly occurring phosphatase tensin homolog ( PTEN ) tumor-suppressor gene inactivation. In first stage our approach, identified 775 N -linked glycoproteins from sera tissue wild-type Pten -null mice. Using label-free...
Accurate classification of breast tumors is vital for patient management decisions and enables more precise cancer treatment. Here, we present a quantitative proteotyping approach based on sequential windowed acquisition all theoretical fragment ion spectra (SWATH) mass spectrometry establish key proteins tumor classification. The study 96 tissue samples representing five conventional subtypes. SWATH proteotype patterns largely recapitulate these subtypes; however, they also reveal varying...
Within a single generation time growing yeast cell imports ∼14 million ribosomal proteins (r-proteins) into the nucleus for ribosome production. After import, it is unclear how these intrinsically unstable and aggregation-prone are targeted to assembly site in nucleolus. Here, we report discovery of conserved nuclear carrier Tsr2 that coordinates transfer r-protein eS26 earliest assembling pre-ribosome, 90S. In vitro studies revealed efficiently dissociates importin:eS26 complexes via an...
Members of the Mycobacterium tuberculosis complex (MTBC) are causative agents in a range mammals, including humans. A key feature MTBC pathogens is their high degree genetic identity yet distinct host tropism. Notably, while bovis highly virulent and pathogenic for cattle, human pathogen M. attenuated cattle. Previous research also suggests that preference amongst members has basis innate immune responses. To explore tropism, we present in-depth profiling reference strains AF2122/97 H37Rv at...
Biocatalysis offers a promising path for plastic waste management and valorization, especially hydrolysable plastics such as polyethylene terephthalate (PET). Microbial whole-cell biocatalysts simultaneous PET degradation growth on monomers would offer one-step solution toward recycling or upcycling. We set out to engineer the industry-proven bacterium Pseudomonas putida (i) metabolism of sole carbon sources, (ii) efficient extracellular expression hydrolases. pursued this approach both...
Abstract The sexual strain of the planarian Schmidtea mediterranea , indigenous to Tunisia and several Mediterranean islands, is a hermaphrodite 1,2 . Here we isolate individual chromosomes use sequencing, Hi-C 3,4 linkage mapping assemble chromosome-scale genome reference. map reveals an extremely low rate recombination on chromosome 1. We confirm suppression 1 by genotyping sperm cells oocytes. show that previously identified genomic regions maintain heterozygosity even after prolonged...
Plants are colonized by a diverse community of microorganisms, the plant microbiota, exhibiting defined and conserved taxonomic structure. Niche separation based on spatial segregation complementary adaptation strategies likely forms basis for coexistence various microorganisms in environment. To gain insights into organism-specific adaptations molecular level, we selected two exemplary members core leaf microbiota profiled their proteomes upon Arabidopsis phyllosphere colonization. The...
We report here an update to the reference genome sequence of bovine tuberculosis bacillus Mycobacterium bovis AF2122/97, generated using integrative multiomics approach. The includes 42 new coding sequences (CDSs), 14 modified annotations, 26 single-nucleotide polymorphism (SNP) corrections, and disclosure that RD900 locus, previously described as absent from genome, is in fact present.
Eukaryotic ribosome precursors acquire translation competence in the cytoplasm through stepwise release of bound assembly factors, and proofreading their functional centers. In case pre-60S, these steps include removal placeholders Rlp24, Arx1 Mrt4 that prevent premature loading ribosomal protein eL24, protein-folding machinery at polypeptide exit tunnel (PET), stalk, respectively. Here, we reveal sequential ATPase GTPase activities license factors Rei1 Yvh1 to trigger removal. Drg1-ATPase...
Abstract Mycobacterium tuberculosis has succeeded as a human pathogen for tens of thousands years thanks to its ability resist and adapt the adverse conditions it encounters upon infection. Bacterial adaptation stress is commonly viewed in context transcriptional regulation, with implicit expectation that an initial transcriptomic response tightly coupled ensuing proteomic response. However, after challenging M . nitric oxide we found rapid responses, detectable within minutes exposure,...
Enhanced transcription of the Rv2660c locus in response to starvation Mycobacterium tuberculosis H37Rv encouraged addition predicted protein an improved vaccine formulation. Using strand-specific RNA sequencing, we show that up-regulated transcript is fact a small encoded on opposite strand annotated Rv2660c. The originates within prophage and expressed only strains carry PhiRv2. contains both host phage sequences provides useful biomarker monitor bacterial during infection and/or...