A5072698789- Fungal and yeast genetics research
- Evolution and Genetic Dynamics
- Fermentation and Sensory Analysis
- Mitochondrial Function and Pathology
- Cancer Genomics and Diagnostics
- Microbial Metabolic Engineering and Bioproduction
- CRISPR and Genetic Engineering
- DNA Repair Mechanisms
- Yeasts and Rust Fungi Studies
- Genomics and Rare Diseases
- Gene Regulatory Network Analysis
- Chromosomal and Genetic Variations
- Genetic Mapping and Diversity in Plants and Animals
- Antibiotic Resistance in Bacteria
- Gene expression and cancer classification
- Genomic variations and chromosomal abnormalities
- RNA Research and Splicing
- Marine Bivalve and Aquaculture Studies
- Biofuel production and bioconversion
- Genetic Neurodegenerative Diseases
- Drug Transport and Resistance Mechanisms
- Sport Psychology and Performance
- Antibiotics Pharmacokinetics and Efficacy
- Sports Performance and Training
- Bioinformatics and Genomic Networks
University of Gothenburg
2016-2024
Sahlgrenska University Hospital
2024
Norwegian University of Life Sciences
2014-2022
The capacity to map traits over large cohorts of individuals-phenomics-lags far behind the explosive development in genomics. For microbes, estimation growth is key phenotype because its link fitness. We introduce an automated microbial phenomics framework that delivers accurate, precise, and highly resolved phenotypes at unprecedented scale. Advancements were achieved through introduction transmissive scanning hardware software technology, frequent acquisition exact colony population size...
Deletion of mitochondrial DNA in eukaryotes is currently attributed to rare accidental events associated with replication or repair double-strand breaks. We report the discovery that yeast cells arrest harmful intramitochondrial superoxide production by shutting down respiration through genetically controlled deletion oxidative phosphorylation genes. show this process critically involves antioxidant enzyme dismutase 2 and two-way mitochondrial-nuclear communication Rtg2 Rtg3. While...
Exposing natural selection driving phenotypic and genotypic adaptive differentiation is an extraordinary challenge. Given that organism's life stages are exposed to the same environmental variations, we reasoned fitness components, such as lag, rate, efficiency of growth, directly reflecting performance in these stages, should often be selected concert. We therefore conjectured correlations between components over isolates, a particular context, would constitute robust signal recent...
Research to date has suggested that both individual marine species and ecological processes are expected exhibit diverse responses the environmental effects of climate change. Evolutionary can occur on rapid (ecological) timescales, yet studies typically do not consider role adaptive evolution will play in modulating biological Investigations into such have been focused at particular levels (e.g., cellular, population, community), often lacking interactions among levels. Since all...
An economically viable production of biofuels and biochemicals from lignocellulose requires microorganisms that can readily convert both the cellulosic hemicellulosic fractions into product. The yeast Candida intermedia displays a high capacity for uptake conversion several lignocellulosic sugars including abundant pentose d-xylose, an underutilized carbon source since most industrially relevant cannot naturally ferment it. Thus, C. constitutes important knowledge genetic information could...
The rapid transmission of antibiotic resistance genes on conjugative plasmids between bacterial host cells is a major cause the accelerating crisis. There are currently no experimental platforms for fast and cost-efficient screening genetic effects by conjugation, which prevents understanding targeting conjugation.
Abstract Hybrids between diverged lineages contain novel genetic combinations but an impaired meiosis often makes them evolutionary dead ends. Here, we explore to what extent aborted followed by a return-to-growth (RTG) promotes recombination across panel of 20 Saccharomyces cerevisiae and S. paradoxus diploid hybrids with different genomic structures levels sterility. Genome analyses 275 clones reveal that RTG generates extensive regions loss-of-heterozygosity in sterile either defective or...
Clinical genetic laboratories often require a comprehensive analysis of chromosomal rearrangements/structural variants (SVs), from large events like translocations and inversions to supernumerary ring/marker chromosomes small deletions or duplications. Understanding the complexity these their clinical consequences requires pinpointing breakpoint junctions resolving derivative chromosome structure. This task surpasses capabilities short-read sequencing technologies. In contrast, long-read...
Abstract Adaptive evolution of clonally dividing cells and microbes is the ultimate cause cancer infectious diseases. The possibility constraining adaptation cell populations, by inhibiting proteins enhancing evolvability, has therefore attracted interest. However, our current understanding how genes influence kinetics limited, partly because accurately measuring for many populations challenging. We used a high-throughput adaptive laboratory platform to track >18,000 corresponding...
Abstract A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us develop a theoretical–experimental framework disclosing presence such adaptation‐speeding mechanisms in an experimental evolution setting circumventing need pursuing costly mutation–accumulation experiments. To this end, we exposed clonal populations budding yeast whole range stressors. By growth phenotyping, found...
The mutational processes dictating the accumulation of mutations in genomes are shaped by genetic background, environment and their interactions. Accurate quantification mutation rates spectra under drugs has important implications disease treatment. Here, we used whole-genome sequencing time-resolved growth phenotyping yeast lines to give a detailed view mutagenic effects rapamycin hydroxyurea on genome cell growth. Mutation depended backgrounds but were only marginally affected rapamycin....
ABSTRACT The rapid horizontal transmission of many antibiotic resistance genes between bacterial host cells on conjugative plasmids is a major cause the accelerating crisis. Preventing understanding and targeting conjugation, there currently are no experimental platforms for fast cost-efficient screening genetic effects by conjugation. We introduce novel framework to screen conjugation based >60.000 pairs cell populations in parallel. Plasmid-carrying donor strains constructed high...
Summary Most organisms’ traits result from the complex interplay of many genetic and environmental factors, making their prediction genotypes difficult. Here, we used machine learning models to explore genotype-phenotype connections for 223 life history measured across 1011 genome-sequenced Saccharomyces cerevisiae strains. Firstly, genome-wide association studies connect variants with phenotypes. Next, benchmarked an automated pipeline that includes preprocessing, feature selection,...
Abstract Hybrids between species or diverged lineages contain fundamentally novel genetic combinations but an impaired meiosis often makes them evolutionary dead ends. Here, we explored to what extent and how aborted followed by a return-to-growth (RTG) promotes recombination across panel of 20 yeast diploid backgrounds with different genomic structures levels sterility. Genome analyses 284 clones revealed that RTG promoted generated extensive regions loss-of-heterozygosity in sterile...
Abstract Deletion of mitochondrial DNA in eukaryotes is mainly attributed to rare accidental events associated with replication or repair double-strand breaks. We report the discovery that yeast cells arrest harmful intramitochondrial superoxide production by shutting down respiration through genetically controlled deletion oxidative phosphorylation genes. show regulatory circuitry underlying this editing critically involves antioxidant enzyme dismutase 2 and two-way mitochondrial-nuclear...
ABSTRACT Adaptive evolution of clonally dividing cells and microbes is the ultimate cause cancer infectious diseases. The possibility constraining adaptation cell populations, by inhibiting proteins that enhance their evolvability has therefore attracted substantial interest. However, our current understanding how individual genes influence speed limited, partly because accurately tracking for many experimental populations in parallel challenging. Here we use a high throughput artificial...
Summary The mutational processes dictating the accumulation of mutations in genomes are shaped by genetic background, environment and their interactions. Accurate quantification mutation rates spectra under drugs has important implications disease treatment. Here, we used whole-genome sequencing time-resolved growth phenotyping yeast lines to give a detailed view mutagenic effects rapamycin hydroxyurea on genome cell growth. Mutation depended backgrounds, but were only marginally affected...
Background: Clinical genetic laboratories often require comprehensive analysis of chromosomal rearrangements/structural variants (SVs) which can range from gross events, such as translocations and inversions, to supernumerary ring/marker chromosomes, small deletions or duplications. To fully understand the complexity a specific event its associated clinical consequences, it is imperative locate breakpoint junctions resolve derivative chromosome structure. This task, however, surpasses...
Age-related diseases are intimately linked to mitochondrial impairment. Whether oxidative stress is a major driver of this impairment still contentious issue. Here we show that yeast cells adapt intramitochondrial superoxide anion ( ) production beyond antioxidant defenses by swiftly reducing the copy numbers electron transport chain (ETC) genes, while maintaining undeleted mtDNA. The ETC genes rapidly restored after cessation short-term stress, whereas long-term causes irreversible loss...
ABSTRACT Adaptive Laboratory Evolution (ALE) of microbes can improve the efficiency sustainable industrial processes important to global economy, but chance and genetic background effects often lead suboptimal outcomes. Here we report an ALE platform circumvent these flaws through parallelized clonal evolution at unprecedented scale. Using this platform, clonally evolved 10 ^4 yeast populations in parallel from many strains for eight desired wine production traits. Expansions both replicates...