A5063536926- Photosynthetic Processes and Mechanisms
- Cassava research and cyanide
- Ubiquitin and proteasome pathways
- Protist diversity and phylogeny
- Nematode management and characterization studies
- Advanced Proteomics Techniques and Applications
- Plant Virus Research Studies
- Plant Micronutrient Interactions and Effects
- Plant nutrient uptake and metabolism
- Plant Molecular Biology Research
- Light effects on plants
- Plant Pathogenic Bacteria Studies
- Algal biology and biofuel production
- SARS-CoV-2 detection and testing
- Genomics and Phylogenetic Studies
- SARS-CoV-2 and COVID-19 Research
- Banana Cultivation and Research
- Microbial Metabolic Engineering and Bioproduction
- Machine Learning in Bioinformatics
- Metabolism, Diabetes, and Cancer
- Bioinformatics and Genomic Networks
- Genetics, Bioinformatics, and Biomedical Research
- Bacteriophages and microbial interactions
- Infection Control and Ventilation
- Plant Gene Expression Analysis
University Hospital of Basel
2023-2024
University of Basel
2024
ETH Zurich
2017-2022
Carnegie Institution for Science
2017
École Polytechnique Fédérale de Lausanne
2009
Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most these have not yet been elucidated. To engineer improve metabolic traits, we need comprehensive accurate knowledge organization regulation plant at genome scale. Here, present a computational pipeline identify enzymes, pathways, gene clusters from sequenced genome. Using this pipeline, generated pathway...
Summary Protein phosphorylation and acetylation are the two most abundant post‐translational modifications ( PTM s) that regulate protein functions in eukaryotes. In plants, these s have been investigated individually; however, their co‐occurrence dynamics on proteins is currently unknown. Using Arabidopsis thaliana , we quantified changes phosphorylation, abundance leaf rosettes, roots, flowers, siliques seedlings at end of day ED ) night EN ). This identified 2549 phosphorylated 909...
Abstract Background Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava a highly heterozygous with repetitive difficult-to-assemble genome. Findings Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, combination the assembler hifiasm, produced genome assemblies at near complete haplotype resolution higher...
Cassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production widely affected by mosaic disease (CMD), which caused the African geminivirus that transmitted whiteflies. breeders often use a single locus, CMD2, for introducing CMD resistance into susceptible cultivars. The CMD2 locus has been genetically mapped to 10-Mbp region, but its organization genes as well their functions are unknown.We report haplotype-resolved de novo assemblies...
Abstract Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional controls fluctuations at protein level. Here, we report a high‐resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over 12 hr light:12 dark cycle phosphoproteome immediately before after light‐to‐dark dark‐to‐light transitions. We quantified nearly 5,000 proteins 800 phosphoproteins, which 288 fluctuated in their abundance 226...
Phosphorus absorbed in the form of phosphate (H2 PO4- ) is an essential but limiting macronutrient for plant growth and agricultural productivity. A comprehensive understanding how plants respond to starvation development more phosphate-efficient crops. Here we employed label-free proteomics phosphoproteomics quantify protein-level responses 48 h versus phosphite PO3- resupply phosphate-deprived Arabidopsis thaliana suspension cells. Phosphite similarly sensed, taken up transported by cells...
Abstract Cassava mosaic disease (CMD) suppresses cassava yields across the tropics. The dominant CMD2 locus confers resistance to geminiviruses. It has been reported that CMD2-type landraces lose after regeneration through de novo morphogenesis. As full genome bisulfite sequencing failed uncover an epigenetic mechanism for this loss of resistance, whole and genetic variant analysis was performed fine-mapped a 190 kilobase interval. Collectively, these data indicate is caused by...
Reversible protein acetylation occurring on Lys-Ne has emerged as a key regulatory post-translational modification in eukaryotes. It is mediated by two groups of enzymes: lysine acetyltransferases (KATs) and deacetylases (KDACs) that catalyze the addition removal acetyl from target proteins. Estimates indicate second to phosphorylation abundance, with thousands acetylated sites now identified different subcellular compartments. Considering important role phosphorylation, elucidating...
Abstract The prediction of functional domains is typically among the first steps towards understanding function new proteins and protein families. There are numerous databases annotated that permit researchers to identify on individual interest. However, it necessary perform high-throughput domain searches gain evolutionary insight into functions Unfortunately, at present, difficult search for, visualize conservation across multiple and/or groups in an intuitive manner. Here we present...
Abstract The implementation of isolation precautions for patients with suspected Coronavirus Disease 2019 (COVID-19) and pending test results is resource intensive. Due to the limited availability single-bed rooms at our institution, we isolated COVID-19 together without on-site in multiple-bed until SARS-CoV-2-test were available. We evaluated likelihood SARS-CoV-2 transmission individuals sharing room on-site. This observational study was performed University Hospital Basel, Switzerland,...
Abstract Background During the SARS-CoV-2 pandemic, many countries directed substantial resources towards genomic surveillance to detect and track viral variants. There is a debate over how much sequencing effort necessary in national programs for future pandemic threats. Aim We aimed investigate effect of reduced on outcomes large dataset from Switzerland, comprising more than 143k sequences. Methods employed uniform downsampling strategy using 100 iterations each effects fewer available...
ABSTRACT Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional controls fluctuations at protein-level. Here we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over 12 h light : dark cycle phosphoproteome immediately before after light-to-dark dark-to-light transitions. We quantified nearly 5000 proteins 800 phosphoproteins, which 288 fluctuated in their abundance 226...
SUMMARY Phosphorus absorbed in the form of phosphate (H 2 PO 4 − ) is an essential but limiting macronutrient for plant growth and agricultural productivity. A comprehensive understanding how plants respond to starvation develop more phosphate-efficient crops. Here we employed label-free proteomics phosphoproteomics quantify protein-level responses 48 h versus phosphite 3 resupply phosphate-deprived Arabidopsis thaliana suspension cells. Phosphite similarly sensed, taken up, transported by...
Abstract Background Cassava ( Manihot esculenta ) is an important clonally propagated food crop in tropical and sub-tropical regions worldwide. Genetic gain by molecular breeding limited because cassava has a highly heterozygous, repetitive difficult to assemble genome. Findings Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution higher continuity accuracy...
Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional controls fluctuations at protein-level. Here we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over 12 h light : dark cycle phosphoproteome immediately before after light-to-dark dark-to-light transitions. We quantified nearly 5000 proteins 800 phosphoproteins, which 288 fluctuated in their abundance 226 phosphorylation...